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	<title><![CDATA[BOL: Related items]]></title>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/21096/how-to-prepare-your-bioinformatics-cv</guid>
	<pubDate>Mon, 09 Feb 2015 01:50:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/21096/how-to-prepare-your-bioinformatics-cv</link>
	<title><![CDATA[How to Prepare your Bioinformatics CV ?]]></title>
	<description><![CDATA[<p>Preparing a CV is also an art as well as a requirement for a person applying for a job .<br /> Curriculum Vitae is the first impression on the employer so it should be the best.How It can be the best can be learnt.Here is a link where you can get guidelines on how CV can be prepared and a sample also. Preparing your own Curriculum Vitae can seem a daunting task, quite apart from what to put in and what to leave out, describing your own strengths and abilities isn't easy. What we have tried to do with the following guidelines is to make the whole process a much easier one and ensure that you end up with a professional document which shows you how to pitch your skills and stand out from the crowd. In the current economic and employment climate, employers are looking to consistently improve on productivity and match a prospective employee's skills and experience with the job needs, both now and in the future.<br /> <strong><br /> Presentation and layout</strong><br /> Always ensure that your CV is laser-printed on white, good quality paper, use a clean typeface and don't go smaller than 12 point.<br /> The use of sub-headings (e.g. Personal details, career history, etc.) will help potential employers glean the information they require with ease.<br /> There should be clear spaces between category headings for easy clarification and definition.<br /> Your name, address and phone number(s) should form the start of the document. If you are giving a work number add the following - 'please use with discretion.'<br /> Commencing with your present or most recent employer, state your career history. Then list your professional qualifications. If you have been working for many years list your academic qualifications and a very brief mention as to your college or schooling.<br /> If you are just commencing your working life, having previously been a student, provide more in depth knowledge regarding your academic achievements to date.<br /> <br /> <strong>Content</strong></p><p>Starting with your current or most recent employment provide details of your position as follows:</p><ul>
<li>A chronological CV should be arranged in reverse chronological order. It should be apparent immediately where you are now.</li>
<li>Remember that an application form is limited to the few things that a particular institution wants to know about everybody. A CV lets you give information that is unique to you. Add all your key accomplishments and activities in the initial draft. In subsequent drafts, you can remove information that may not be pertinent.</li>
<li>Resist the temptation to append explanatory sentences or language, which will distract the reader from the basic information being presented. The language of a CV is abbreviated and succinct. When applying for residency training, you will have the opportunity to express yourself in a personal or biographical statement. In the future, when applying for a job or some other type of position, you will want to include an appropriate cover letter with your CV to explain your particular qualifications and strengths for the position.</li>
<li>Don&rsquo;t despair if your CV doesn&rsquo;t resemble those of other students who are applying to the same residency program. Everybody&rsquo;s CV is different. Even if everyone used the same format suggested in this section, your CV will not resemble others&rsquo; because it doesn&rsquo;t have the same content. No residency program director is looking for a specific CV style. You will receive points for neatness, and readability.</li>
<li>Be honest. If you haven&rsquo;t accomplished anything in a particular category, leave it out. Don&rsquo;t create accomplishments to fill in the spaces. You can be specific about your level of participation in a project or activity, but don&rsquo;t be misleading (i.e., you can say you coordinated membership recruitment for your AMSA chapter, but don&rsquo;t say you were &ldquo;president&rdquo; unless you were).</li>
</ul><ul>
<li>Job title - time that you have held this position</li>
<li>The key tasks and responsibilities that comprise this role's requirements - notable achievements whilst in the role</li>
<li>Where possible quantify your achievements with precise facts and figures, e.g. managed junior staff, handled department budget, prepared management reports</li>
<li>Expand on the skills you are using in your current job which you believe will be valuable in the position(s) for which you are applying</li>
</ul><p>It is not necessary to state the reason you are leaving your current position. This will be a topic for conversation when you are invited for interview or can be covered in your letter of application.<br /> For all previous employment, unless one appointment was more significant than your current or last position, keep details brief i.e. the name of the company, job title, period of employment and the job.<br /> Be sure there are no gaps in your career history - unless for example you took a year out to travel, in which case make reference to this under Interests/Hobbies.<br /> If you are a student just starting work, give any evidence you can to demonstrate your practical skills e.g. school prefect, event organisation, member of sports team, contributor to college magazine or voluntary work.<br /><br /> You are under no obligation to disclose marital status, age or whether or not you have children unless these are specific criteria for selection for a position that you are interested in.<br /> Consider what examples (interests/ hobbies) you can give to show that you match the selection criteria.<br /><br /> If they want someone to work as part of a large team, remember to say if you belong to a local organisation or if you are part of a sports team.<br /><br /> If they want someone who will work on their own for large periods of time, make reference to an Open University course you are considering undertaking.<br /><br /> Your primary objective is to convince the prospective employer that you have the requisite skills, experience and hunger to do the job.<br /><br /> Your CV should be no more than two A4 pages and as every employer is different remember to customise your CV to every job you go after.</p><p>There are abundant books on the contents and presentation of a general CV. A BMJ article published in 1978, offering doctors guidance on how to prepare a CV, has been reprinted in the widely read How to do it series.1 2 A survey among postgraduate deans and training advisers at regional colleges found that the contents and presentation of a model CV for doctors in training has been published.3 It is perhaps surprising to note that these models differ significantly from one another. Although they may be useful as starting points, their differences tend to create confusion and anxiety among students. I would argue that these differences exist because the content and presentation of the "ideal" CV vary considerably among individual applicants, the stage of their careers, and the purposes for which the CV is used. It is impossible to create a generic CV. I have therefore not attempted to draw up another model CV. Rather, the purpose of this article is to outline the general principles and important practical points in preparing a good CV. General principles on contents Before finalising your CV for a particular purpose you must be sure of your objectives, whether it is used as an initial screening or the only selection instrument, and the criteria against which it is judged. What details, and how many of them, to include in your CV depends on these factors. I shall illustrate with examples relevant to medical students.&nbsp;<br /> <br /> (1) Job application Your objective is to get the job. In a job application, the CV is used for two purposes: as an initial screening instrument for shortlisting candidates and as a framework for discussion during the interview. The explicit criteria used for shortlisting are usually given in the job advertisement. For some organisations, separate lists of essential and desirable criteria are given. Alternatively, you can get a good idea of the basic requirements from the job description. Your CV must clearly highlight these criteria, preferably on the first page. These usually include: formal qualifications; registration with the General Medical Council; and the prescribed experience. It is sometimes easy to forget to mention items specifically asked for in the job description (for example, a valid driving licence). The implicit criteria are less easy to pinpoint. For example, how much detail on your BSc dissertation and publications should you include? Should you make a long list of extracurricular activities, interests outside medicine, and positions of responsibility? If you admit to a wide range of extracurricular activities and interests, would you be considered as a candidate with a well balanced mature personality or will it be interpreted to mean that you will have little time or interest to do your job? There are no easy answers. Common sense might tell you that BSc dissertation and publications are more important in application for teaching hospital or research posts, but less important for district hospital posts. Conversely, you might think that interests outside medicine are more important for posts in district hospitals or in general practice. This is, however, not always true. A few consultants at district hospital are highly academic. Information gathered from students and doctors working under the professor or consultant concerned may be vital. Alternatively, it is worth while doing your homework by looking up your prospective consultant in the medical directory. This may occasionally prompt you to include information that you might otherwise have left out. For example, you may find that the consultant qualified in Scotland and has previously worked in Scotland for a considerable time, and you may decide to add in your CV that you studied in a Scottish secondary school. Since the CV is only used as for initial screening, you need not go into your previous experience or extracurricular activities in too much detail. Highlight only the most significant points, and leave the details for the interview. If you are applying for a clinical post, one of your referees should be a consultant for whom you have worked as a student. You should ask for permission to use his/her name before submitting your application.&nbsp;<br /> <br /> (2) Application for research scholarship or PhD studentship The CV and application form are sometimes used as the sole selection instrument, and you must make enquiries before you submit your application. Clearly, academic ability is the main criterion for selection, and you should include as much information relevant to your academic ability and interests as you can. Examples are your A levels, your BSc dissertation, any publications (even in the form of a letter in newspaper), any experience as an editor (for example, for your school magazine). Your extracurricular activities are less important, and you can simply give a short list. At least one of the referees should be an academic - for example, your previous supervisor in your BSc degree.<br /> &nbsp;<br /> (3) Application to join a clinical course in another medical school Preclinical students who have completed an intercalated degree often have the option of applying to join a clinical course in another medical school, although it may become more difficult to do so with the introduction of the new GMC curriculum. Your CV is usually used for shortlisting candidates for interview. The criteria differ slightly among medical schools, but both academic ability and contribution to university life are important. Hence, not only should you highlight your academic achievements but you must also highlight your participation in the university (for example, in sports or music).&nbsp;<br /> <br /> (4) For the information of your tutor or counsellor For most medical schools, you are allocated a tutor who provides both academic and non-academic support and monitors your progress throughout your study on a confidential basis. Students are sometimes asked to submit their up to date CV to their tutors for information. Assuming that the tutors are helpful there is little to gain from over emphasising your strengths or hiding your weaknesses. Once you become a doctor in training after you qualify you will need to undergo an annual assessment of your progress. It serves to certify that you have reached a satisfactory standard, but it is also used as an aid to identify and help with your weaknesses. You may find it difficult to balance these two purposes in presenting your CV. General principles on presentation Now that all students are computer literate, there should be few problems in preparing a well presented CV. The following list serves as a reminder on how to present your CV effectively: Spelling or grammar mistakes - do not rely purely on the spell check on your computer. Ask friends to proofread your CV for you. Consistency - The use of punctuation to open and close sentences, justification, and fonts should be consistent. Readability - The headings should be clear. The font size should be no less than 12 point. Basic criteria - The basic criteria should be easily located, preferably on the first page. Length - The length of your CV increases as you progress up the professional ladder. For students, it should generally be no more than three pages. Quality of print - The CV should be printed on good quality paper, preferably using a laser printer. Practical points In this article, I argue that different versions of a CV may be required for different purposes. Even applications for different posts in the same specialty may require slightly different versions. Also, CVs need to be updated regularly. This would have been time consuming to achieve in the past, but it is now quite simple, with the aid of a basic word processing package. A master CV containing all relevant information should be prepared and saved as a computer file. This should be continuously kept up to date. When the need for a CV arises, it can be tailormade by editing the master document. It is important to save each of these edited versions separately, with the file names indicating the date when it was created and the purpose. It is also important to prepare a cover letter to go with the CV. Key messages A good CV is essential for successful progression up the medical professional ladder The contents of the CV should be tailormade for the purpose it is used for and the criteria against which it is judged. It is important to gather information about these criteria first The CV must be technically well presented, with the basic criteria easily located Information technology has made it simple to regularly update our CVs and allows preparation of different versions of a CV for different purposes with relative ease.</p><p><strong>Reference:</strong></p><p>Prepare a curriculum vitae. BMJ 1978;25(2):1478-9.<br /> O'Brien E. Prepare a curriculum vitae. In: Reece D, ed.&nbsp;<br /> How to do it. Vol 1. London: BMJ Publishing Group, 1995 Chambler AF, Chapman-Sheath PJ, Pearse MF.&nbsp;<br /> A model curriculum vitae: what are the trainers looking for? Hosp Med 1998;59(4):324-6.</p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/21365/a-guide-for-complete-r-beginners</guid>
	<pubDate>Fri, 20 Feb 2015 23:36:46 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/21365/a-guide-for-complete-r-beginners</link>
	<title><![CDATA[A guide for complete R beginners !]]></title>
	<description><![CDATA[<p>This tutorial is intended to introduce users quickly to the basics of R, focusing on a few common tasks that &nbsp;biologists need to perform &nbsp;some basic analysis: &nbsp;load a table, plot some graphs, and perform some basic statistics. More extensive tutorials can be found on the project website and via bioconductor (not covered here).</p><p><em><span style="text-decoration: underline;">R-language: </span></em><a href="http://www.r-project.org/"><span style="color: #000080;"><span style="text-decoration: underline;"><em>http://www.</em></span></span><span style="color: #000080;"><span style="text-decoration: underline;"><em><strong>r</strong></em></span></span><span style="color: #000080;"><span style="text-decoration: underline;"><em>-project.org</em></span></span></a></p><p><em>BioConductor</em>:&nbsp;<a href="http://www.bioconductor.org/">http://www.bioconductor.org</a></p><p><strong>Advantages of R</strong></p><ul>
<li>Free!</li>
<li>Powerful, many libraries have been created to perform application specific tasks. e.g. analysis of microarray experiments and Next-Gen sequencing (bioconductor: including Bioseq group).</li>
<li>Presentation quality graphics
<ul>
<li>Save as a png, pdf or svg</li>
</ul>
</li>
<li>History
<ul>
<li>What you do can be saved for the next time you use R.</li>
<li>Ability to turn it into an automated script to perform again and again on different data</li>
</ul>
</li>
</ul><p><strong>Disadvantages</strong></p><ul>
<li>Lack of a comprehensive graphical user interface, but two do exist: However some do exist:&nbsp;R commander: <a href="http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/">http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/</a> and&nbsp;Limma-gui (microarrays) : <a href="http://bioinf.wehi.edu.au/limmaGUI/">http://bioinf.wehi.edu.au/limmaGUI/</a></li>
</ul><p><strong>Preparation</strong></p><ul>
<li>(Optional) Download and save the tutorial data set from
<ul>
<li>http://bioinformatics.knowledgeblog.org/wp-content/uploads/bioinf/kerr/data.tsv</li>
<li>Start R (type R on a Linux or Mac terminal, or find the starting link from PC)</li>
</ul>
</li>
</ul><p><strong>Getting More Help</strong></p><ul>
<li>Project Home page
<ul>
<li><span style="color: #000080;"><span style="text-decoration: underline;"><a href="http://www.r-project.org/">http://www.r-project.org/</a></span></span></li>
<li>Check out the &lsquo;introduction to R&rsquo;, which is a much more in depth guide .</li>
<li>Also R has a built-in help system (see later)</li>
</ul>
</li>
</ul><p><strong>Working directory</strong></p><p>This is the directory used to store your data and results. It is useful if it is also the directory where your input data is stored.</p><ul>
<li>Mac/Linux: this is the directory where you typed in R</li>
<li>PC: Change using the change working directory option</li>
</ul>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21539/research-associate-at-central-potato-research-institute-cpri-shimla-himachal-pradesh</guid>
  <pubDate>Wed, 11 Mar 2015 03:07:37 -0500</pubDate>
  <link></link>
  <title><![CDATA[RESEARCH ASSOCIATE at Central Potato Research Institute (CPRI) - Shimla, Himachal Pradesh]]></title>
  <description><![CDATA[
<p>One post of Research Associate for Project Implementation Unit in the time bound project “XII Plan -–Centre of Agricultural Bio-informatics(CABIN)” are to be filled on purely contractual basis which will be co-terminus with the project as per the details given as under : </p>

<p>No of post : 01 <br />Essential qualifications: i) Ph. D degree in Bioinformatics/computers/Bio-technology. OR ii) Master’s Degree in Bioinformatics/computers/Bio-technology with 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience as evidenced from fellowship/Associateship/training/other engagements. <br />Desirable qualifications: i) Working Knowledge and Published Research papers in Bio-informatics. <br />Monthly emoluments : Rs. 23,000/- + HRA . for M.Sc degree holder Rs. 24,000/- + HRA for Ph.D degree holder <br />Maximum Age limit : Research Associate – Males- 40 years &amp; Women 45 years. <br />SELECTION PROCEDURE FOR CENTRAL POTATO RESEARCH INSTITUTE (CPRI) – RESEARCH ASSOCIATE POST: </p>

<p>Written Test on 20/03/2015. <br />Shortlisted candidates will undertake face to face interview. <br />Dates are yet to be announced for the final selection <br />WALK-IN PROCEDURE FOR RESEARCH ASSOCIATE VACANCY IN CENTRAL POTATO RESEARCH INSTITUTE (CPRI): </p>

<p>Interested/eligible candidates should submit their application along with the attested copies of educational qualification (provisional degree of Masters and Ph.D is mandatory )/experience certificates and one passport size photograph to the Asstt. Admn. Officer(E-I), CPRI, Shimla-171001 at 9.30 AM on the date of interview. The candidates appearing for interview must bring original certificate with them and only those candidates possessing essential qualification as per advertisement will be interviewed. The Director, CPRI, Shimla reserves the right either to fill up the post or cancel the interview without assigning any reasons thereof. Application form is available in the website ( website: http//cpri.ernet.in). No TA/DA will be given by the Institute to the candidates. The Institute is located at Bemloe which is about 2 Kms from Main Bus Stand(Old)/3 Kms. from the Railway Station and about 5 Kms. from ISBT (Tutikandi).</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/22044/binc-sample-question-paper</guid>
	<pubDate>Thu, 16 Apr 2015 09:12:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/22044/binc-sample-question-paper</link>
	<title><![CDATA[BINC Sample Question Paper !!!]]></title>
	<description><![CDATA[<p>BINC sample question paper for round ONE.</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/22044" length="1260" type="text/plain" />
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/22068/binc-examination-2015</guid>
	<pubDate>Fri, 17 Apr 2015 03:34:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/22068/binc-examination-2015</link>
	<title><![CDATA[BINC examination 2015 !!!]]></title>
	<description><![CDATA[<p>BioInformatics National Certification (BINC) Examination 2015 organized by Department of Biotechnology, Government of India, New Delhi Pondicherry University, Puducherry</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/22068" length="281577" type="application/pdf" />
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/22403/ryan-e-mills-lab</guid>
  <pubDate>Tue, 26 May 2015 09:29:24 -0500</pubDate>
  <link></link>
  <title><![CDATA[Ryan E. Mills Lab]]></title>
  <description><![CDATA[
<p>Our research group is primarily focused on the analysis of whole genome sequence data to identify genetic variation (primarily structural variation) and examine their potential functional impact in disease phenotypes. We are particularly interested in analyzing complex regions of the genome that are not easily resolved through modern sequencing approaches and which may exhibit interesting mechanistic origins.</p>

<p>We are also interested in the large-scale integration of genomic, expression, methylation and proteomic data sets, as well as the application of whole genome sequence analysis in clinical diagnostics. </p>

<p>More at http://millslab.ccmb.med.umich.edu/index.html</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/22571/pattern-matching-problem-solution-with-perl</guid>
	<pubDate>Tue, 09 Jun 2015 23:58:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/22571/pattern-matching-problem-solution-with-perl</link>
	<title><![CDATA[Pattern Matching Problem Solution with Perl]]></title>
	<description><![CDATA[<p>Problem at http://rosalind.info/problems/1c/</p><p>#Find all occurrences of a pattern in a string.<br />#Given: Strings Pattern and Genome.<br />#Return: All starting positions in Genome where Pattern appears as a substring. Use 0-based indexing.<br /><br />use strict;<br />use warnings;<br /><br />my $string="GATATATGCATATACTT";<br />my $subStr="ATAT";<br />my $kmer=length($subStr);<br /><br />kmerMatch ($string, $subStr, $kmer);<br /><br />sub kmerMatch { #Check the exact matching kmers with sliding window<br />my ($string, $myStr, $kmer)=@_;<br />for (my $aa=0; $aa&lt;=(length($string)-$kmer); $aa++) {<br />&nbsp;&nbsp;&nbsp; my $myWin=substr&nbsp; $string, $aa,$kmer;<br />&nbsp;&nbsp;&nbsp; if ($myWin eq $myStr) {<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #print "$myWin eq $myStr\n";<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; print $aa;<br />&nbsp;&nbsp;&nbsp; }<br />}<br />}</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/22807/software-packages-for-next-gen-sequence-analysis</guid>
	<pubDate>Fri, 19 Jun 2015 21:07:15 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/22807/software-packages-for-next-gen-sequence-analysis</link>
	<title><![CDATA[Software packages for next gen sequence analysis]]></title>
	<description><![CDATA[<p><strong>Integrated solutions</strong><br /> * <a href="http://www.clcbio.com/index.php?id=1240" target="_blank">CLCbio Genomics Workbench</a> - <em>de novo</em> and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Windows, Mac OS X and Linux.<br /> * <a href="http://g2.trac.bx.psu.edu/" target="_blank">Galaxy</a> - Galaxy = interactive and reproducible genomics. A job webportal.<br /> * <a href="http://www.genomatix.de/products/index.html" target="_blank">Genomatix</a> - Integrated Solutions for Next Generation Sequencing data analysis.<br /> * <a href="http://www.jmp.com/software/genomics/" target="_blank">JMP Genomics</a> - Next gen visualization and statistics tool from SAS. They are <a href="http://www.marketwatch.com/news/story/JMPR-Genomics-NCGR-Partnership-Foster/story.aspx?guid=%7B7AC9DE36-B6AA-4EDE-9CD5-633B29FE6154%7D" target="_blank">working with NCGR</a> to refine this tool and produce others.<br /> * <a href="http://softgenetics.com/NextGENe.html" target="_blank">NextGENe</a> - <em>de novo</em> and reference assembly of Illumina, SOLiD and Roche FLX data. Uses a novel Condensation Assembly Tool approach where reads are joined via "anchors" into mini-contigs before assembly. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Win or MacOS.<br /> * <a href="http://www.dnastar.com/products/SMGA.php" target="_blank">SeqMan Genome Analyser</a> - Software for Next Generation sequence assembly of Illumina, Roche FLX and Sanger data integrating with Lasergene Sequence Analysis software for additional analysis and visualization capabilities. Can use a hybrid templated/de novo approach. Commercial. Win or Mac OS X.<br /> * <a href="http://1001genomes.org/downloads/shore.html" target="_blank">SHORE</a> - SHORE, for Short Read, is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer. A suite created by the 1001 Genomes project. Source for POSIX.<br /> * <a href="http://www.realtimegenomics.com/" target="_blank">SlimSearch</a> - Fledgling commercial product.<br /> <br /> <strong>Align/Assemble to a reference</strong><br /> * <a href="https://secure.genome.ucla.edu/index.php/BFAST" target="_blank">BFAST</a> - Blat-like Fast Accurate Search Tool. Written by Nils Homer, Stanley F. Nelson and Barry Merriman at UCLA.<br /> * <a href="http://bowtie-bio.sourceforge.net/" target="_blank">Bowtie</a> - Ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Uses a Burrows-Wheeler-Transformed (BWT) index. <a href="http://seqanswers.com/forums/showthread.php?t=706" target="_blank">Link to discussion thread here</a>. Written by Ben Langmead and Cole Trapnell. Linux, Windows, and Mac OS X.<br /> * <a href="http://maq.sourceforge.net/" target="_blank">BWA</a> - Heng Lee's BWT Alignment program - a progression from Maq. BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence. C++ source.<br /> * <a href="http://bioinfo.cgrb.oregonstate.edu/docs/solexa/" target="_blank">ELAND</a> - Efficient Large-Scale Alignment of Nucleotide Databases. Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine.<br /> * <a href="http://www.ebi.ac.uk/%7Eguy/exonerate/" target="_blank">Exonerate</a> - Various forms of pairwise alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX.<br /> * <a href="http://1001genomes.org/downloads/genomemapper.html" target="_blank">GenomeMapper</a> - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. A tool created by the 1001 Genomes project. Source for POSIX.<br /> * <a href="http://www.gene.com/share/gmap/" target="_blank">GMAP</a> - GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences. Developed by Thomas Wu and Colin Watanabe at Genentec. C/Perl for Unix.<br /> * <a href="http://dna.cs.byu.edu/gnumap/" target="_blank">gnumap</a> - The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. It seeks to align reads from nonunique repeats using statistics. From authors at Brigham Young University. C source/Unix.<br /> * <a href="http://sourceforge.net/projects/maq/" target="_blank">MAQ</a> - Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina with preliminary functions to handle ABI SOLiD data. Written by Heng Li from the Sanger Centre. Features extensive supporting tools for DIP/SNP detection, etc. C++ source<br /> * <a href="http://bioinformatics.bc.edu/marthlab/Mosaik" target="_blank">MOSAIK</a> - MOSAIK produces gapped alignments using the Smith-Waterman algorithm. Features a number of support tools. Support for Roche FLX, Illumina, SOLiD, and Helicos. Written by Michael Str&ouml;mberg at Boston College. Win/Linux/MacOSX<br /> * <a href="http://mrfast.sourceforge.net/" target="_blank">MrFAST and MrsFAST</a> - mrFAST &amp; mrsFAST are designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. Robust to INDELs and MrsFAST has a bisulphite mode. Authors are from the University of Washington. C as source.<br /> * <a href="http://mummer.sourceforge.net/" target="_blank">MUMmer</a> - MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Released as a package providing an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. Version 3.0 was developed by Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu and Steven L Salzberg - most of whom are at The Institute for Genomic Research in Maryland, USA. POSIX OS required.<br /> * <a href="http://www.novocraft.com/index.html" target="_blank">Novocraft</a> - Tools for reference alignment of paired-end and single-end Illumina reads. Uses a Needleman-Wunsch algorithm. Can support Bis-Seq. Commercial. Available free for evaluation, educational use and for use on open not-for-profit projects. Requires Linux or Mac OS X.<br /> * <a href="http://pass.cribi.unipd.it/cgi-bin/pass.pl" target="_blank">PASS</a> - It supports Illumina, SOLiD and Roche-FLX data formats and allows the user to modulate very finely the sensitivity of the alignments. Spaced seed intial filter, then NW dynamic algorithm to a SW(like) local alignment. Authors are from CRIBI in Italy. Win/Linux.<br /> * <a href="http://rulai.cshl.edu/rmap/" target="_blank">RMAP</a> - Assembles 20 - 64 bp Illumina reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics). POSIX OS required.<br /> * <a href="http://biogibbs.stanford.edu/%7Ejiangh/SeqMap/" target="_blank">SeqMap</a> - Supports up to 5 or more bp mismatches/INDELs. Highly tunable. Written by Hui Jiang from the Wong lab at Stanford. Builds available for most OS's.<br /> * <a href="http://compbio.cs.toronto.edu/shrimp/" target="_blank">SHRiMP</a> - Assembles to a reference sequence. Developed with Applied Biosystem's colourspace genomic representation in mind. Authors are Michael Brudno and Stephen Rumble at the University of Toronto. POSIX.<br /> * <a href="http://www.bcgsc.ca/platform/bioinfo/software/slider" target="_blank"><span style="text-decoration: underline;">Slider</span></a>- An application for the Illumina Sequence Analyzer output that uses the probability files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Authors are from BCGSC. Paper is <a href="http://seqanswers.com/forums/showthread.php?t=740" target="_blank">here</a>.<br /> * <a href="http://soap.genomics.org.cn/" target="_blank">SOAP</a> - SOAP (Short Oligonucleotide Alignment Program). A program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The updated version uses a BWT. Can call SNPs and INDELs. Author is Ruiqiang Li at the Beijing Genomics Institute. C++, POSIX.<br /> * <a href="http://www.sanger.ac.uk/Software/analysis/SSAHA/" target="_blank">SSAHA</a> - SSAHA (Sequence Search and Alignment by Hashing Algorithm) is a tool for rapidly finding near exact matches in DNA or protein databases using a hash table. Developed at the Sanger Centre by Zemin Ning, Anthony Cox and James Mullikin. C++ for Linux/Alpha.<br /> * <a href="http://socs.biology.gatech.edu/" target="_blank">SOCS</a> - Aligns SOLiD data. SOCS is built on an iterative variation of the Rabin-Karp string search algorithm, which uses hashing to reduce the set of possible matches, drastically increasing search speed. Authors are Ondov B, Varadarajan A, Passalacqua KD and Bergman NH.<br /> * <a href="http://bibiserv.techfak.uni-bielefeld.de/swift/welcome.html" target="_blank">SWIFT</a> - The SWIFT suit is a software collection for fast index-based sequence comparison. It contains: SWIFT &mdash; fast local alignment search, guaranteeing to find epsilon-matches between two sequences. SWIFT BALSAM &mdash; a very fast program to find semiglobal non-gapped alignments based on k-mer seeds. Authors are Kim Rasmussen (SWIFT) and Wolfgang Gerlach (SWIFT BALSAM)<br /> * <a href="http://synasite.mgrc.com.my:8080/sxog/NewSXOligoSearch.php" target="_blank">SXOligoSearch</a> - SXOligoSearch is a commercial platform offered by the Malaysian based <a href="http://www.synamatix.com/" target="_blank">Synamatix</a>. Will align Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms. Web Portal. OS independent.<br /> * <a href="http://www.vmatch.de/" target="_blank">Vmatch</a> - A versatile software tool for efficiently solving large scale sequence matching tasks. Vmatch subsumes the software tool REPuter, but is much more general, with a very flexible user interface, and improved space and time requirements. Essentially a large string matching toolbox. POSIX.<br /> * <a href="http://www.bioinformaticssolutions.com/products/zoom/index.php" target="_blank">Zoom</a> - ZOOM (Zillions Of Oligos Mapped) is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis. ZOOM is developed to be highly accurate, flexible, and user-friendly with speed being a critical priority. Commercial. Supports Illumina and SOLiD data.<br /> <br /> <strong><em>De novo</em> Align/Assemble</strong><br /> * <a href="http://www.bcgsc.ca/platform/bioinfo/software/abyss" target="_blank">ABySS</a> - Assembly By Short Sequences. ABySS is a de novo sequence assembler that is designed for very short reads. The single-processor version is useful for assembling genomes up to 40-50 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. By Simpson JT and others at the Canada's Michael Smith Genome Sciences Centre. C++ as source. <br /> * <a href="http://www.broad.mit.edu/science/programs/genome-biology/computational-rd/computational-research-and-development" target="_blank">ALLPATHS</a> - ALLPATHS: De novo assembly of whole-genome shotgun microreads. ALLPATHS is a whole genome shotgun assembler that can generate high quality assemblies from short reads. Assemblies are presented in a graph form that retains ambiguities, such as those arising from polymorphism, thereby providing information that has been absent from previous genome assemblies. Broad Institute.<br /> * <a href="http://www.genomic.ch/edena.php" target="_blank">Edena</a> - Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm. By D. Hernandez, P. Fran&ccedil;ois, L. Farinelli, M. Osteras, and J. Schrenzel. Linux/Win.<br /> * <a href="http://euler-assembler.ucsd.edu/portal/" target="_blank">EULER-SR</a> - Short read <em>de novo</em> assembly. By Mark J. Chaisson and Pavel A. Pevzner from UCSD (published in Genome Research). Uses a de Bruijn graph approach.<br /> * <a href="http://chevreux.org/projects_mira.html" target="_blank">MIRA2</a> - MIRA (Mimicking Intelligent Read Assembly) is able to perform true hybrid de-novo assemblies using reads gathered through 454 sequencing technology (GS20 or GS FLX). Compatible with 454, Solexa and Sanger data. Linux OS required.<br /> * <a href="http://www.seqan.de/projects/consensus.html" target="_blank">SEQAN</a> - A Consistency-based Consensus Algorithm for De Novo and Reference-guided Sequence Assembly of Short Reads. By Tobias Rausch and others. C++, Linux/Win.<br /> * <a href="http://sharcgs.molgen.mpg.de/" target="_blank">SHARCGS</a> - De novo assembly of short reads. Authors are Dohm JC, Lottaz C, Borodina T and Himmelbauer H. from the Max-Planck-Institute for Molecular Genetics.<br /> * <a href="http://www.bcgsc.ca/platform/bioinfo/software/ssake" target="_blank">SSAKE</a> - The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. Authors are Ren&eacute; Warren, Granger Sutton, Steven Jones and Robert Holt from the Canada's Michael Smith Genome Sciences Centre. Perl/Linux.<br /> * <a href="http://soap.genomics.org.cn/" target="_blank">SOAPdenovo</a> - Part of the SOAP suite. See above. <br /> * <a href="https://sourceforge.net/projects/vcake" target="_blank">VCAKE</a> - De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE.<br /> * <a href="http://www.ebi.ac.uk/%7Ezerbino/velvet/" target="_blank">Velvet</a> - Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Need about 20-25X coverage and paired reads. Developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). <br /> <br /> <strong>SNP/Indel Discovery</strong><br /> * <a href="http://www.sanger.ac.uk/Software/analysis/ssahaSNP/" target="_blank">ssahaSNP</a> - ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI Sanger reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac<br /> * <a href="http://bioinformatics.bc.edu/marthlab/PbShort" target="_blank">PolyBayesShort</a> - A re-incarnation of the PolyBayes SNP discovery tool developed by Gabor Marth at Washington University. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes. Developers at Boston College. Linux-64 and Linux-32.<br /> * <a href="http://bioinformatics.bc.edu/marthlab/PyroBayes" target="_blank">PyroBayes</a> - PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines. It was designed to assign more accurate base quality estimates to the 454 pyrosequences. Developers at Boston College. <br /> <br /> <strong>Genome Annotation/Genome Browser/Alignment Viewer/Assembly Database</strong><br /> * <a href="http://bioinformatics.bc.edu/marthlab/EagleView" target="_blank">EagleView</a> - An information-rich genome assembler viewer. EagleView can display a dozen different types of information including base quality and flowgram signal. Developers at Boston College.<br /> * <a href="http://www.sanger.ac.uk/Software/analysis/lookseq/" target="_blank">LookSeq</a> - LookSeq is a web-based application for alignment visualization, browsing and analysis of genome sequence data. LookSeq supports multiple sequencing technologies, alignment sources, and viewing modes; low or high-depth read pileups; and easy visualization of putative single nucleotide and structural variation. From the Sanger Centre.<br /> * <a href="http://evolution.sysu.edu.cn/mapview/" target="_blank">MapView</a> - MapView: visualization of short reads alignment on desktop computer. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China. Linux.<br /> * <a href="http://www.bcgsc.ca/platform/bioinfo/software/sam" target="_blank">SAM</a> - Sequence Assembly Manager. Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type. Developers are Rene Warren, Yaron Butterfield, Asim Siddiqui and Steven Jones at Canada's Michael Smith Genome Sciences Centre. MySQL backend and Perl-CGI web-based frontend/Linux. <br /> * <a href="http://staden.sourceforge.net/" target="_blank">STADEN</a> - Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available <a href="https://sourceforge.net/project/show...kage_id=256957" target="_blank">here</a><br /> * <a href="http://www.bcgsc.ca/platform/bioinfo/software/xmatchview" target="_blank">XMatchView</a> - A visual tool for analyzing cross_match alignments. Developed by Rene Warren and Steven Jones at Canada's Michael Smith Genome Sciences Centre. Python/Win or Linux.<br /> <br /> <strong>Counting e.g. CHiP-Seq, Bis-Seq, CNV-Seq</strong><br /> * <a href="http://epigenomics.mcdb.ucla.edu/BS-Seq/download.html" target="_blank">BS-Seq</a> - The source code and data for the "Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA Methylation Patterning" Nature paper by <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?holding=&amp;db=pubmed&amp;cmd=search&amp;term=Shotgun%20Bisulphite%20Sequencing" target="_blank">Cokus et al.</a> (Steve Jacobsen's lab at UCLA). POSIX.<br /> * <a href="http://woldlab.caltech.edu/chipseq/" target="_blank">CHiPSeq</a> - Program used by Johnson et al. (2007) in their Science publication<br /> * <a href="http://tiger.dbs.nus.edu.sg/cnv-seq/" target="_blank">CNV-Seq</a> - CNV-seq, a new method to detect copy number variation using high-throughput sequencing. Chao Xie and Martti T Tammi at the National University of Singapore. Perl/R.<br /> * <a href="http://www.bcgsc.ca/platform/bioinfo/software/findpeaks" target="_blank">FindPeaks</a> - perform analysis of ChIP-Seq experiments. It uses a naive algorithm for identifying regions of high coverage, which represent Chromatin Immunoprecipitation enrichment of sequence fragments, indicating the location of a bound protein of interest. Original algorithm by Matthew Bainbridge, in collaboration with Gordon Robertson. Current code and implementation by Anthony Fejes. Authors are from the Canada's Michael Smith Genome Sciences Centre. JAVA/OS independent. Latest versions available as part of the <a href="http://vancouvershortr.sourceforge.net/" target="_blank">Vancouver Short Read Analysis Package</a><br /> * <a href="http://liulab.dfci.harvard.edu/MACS/" target="_blank">MACS</a> - Model-based Analysis for ChIP-Seq. MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. Written by Yong Zhang and Tao Liu from Xiaole Shirley Liu's Lab. <br /> * <a href="http://www.gersteinlab.org/proj/PeakSeq/" target="_blank">PeakSeq</a> - PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls. a two-pass approach for scoring ChIP-Seq data relative to controls. The first pass identifies putative binding sites and compensates for variation in the mappability of sequences across the genome. The second pass filters out sites that are not significantly enriched compared to the normalized input DNA and computes a precise enrichment and significance. By Rozowsky J et al. C/Perl.<br /> * <a href="http://mendel.stanford.edu/sidowlab/downloads/quest/" target="_blank">QuEST</a> - Quantitative Enrichment of Sequence Tags. Sidow and Myers Labs at Stanford. From the 2008 publication <a href="http://www.ncbi.nlm.nih.gov/pubmed/18711362" target="_blank">Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data</a>. (C++)<br /> * <a href="http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/" target="_blank">SISSRs</a> - Site Identification from Short Sequence Reads. BED file input. Raja Jothi @ NIH. Perl.<br /> **See also <a href="http://seqanswers.com/forums/showthread.php?t=742" target="_blank">this thread</a> for ChIP-Seq, until I get time to update this list.<br /> <br /> <strong>Alternate Base Calling</strong><br /> * <a href="http://svitsrv25.epfl.ch/R-doc/library/Rolexa/html/00Index.html" target="_blank">Rolexa</a> - R-based framework for base calling of Solexa data. Project <a href="http://www.biomedcentral.com/1471-2105/9/431" target="_blank">publication</a><br /> * <a href="http://hannonlab.cshl.edu/Alta-Cyclic/main.html" target="_blank">Alta-cyclic</a> - "a novel Illumina Genome-Analyzer (Solexa) base caller"<br /> <br /> <strong>Transcriptomics</strong><br /> * <a href="http://woldlab.caltech.edu/rnaseq/" target="_blank">ERANGE</a> - Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Supports Bowtie, BLAT and ELAND. From the Wold lab.<br /> * <a href="http://www.genoscope.cns.fr/externe/gmorse/" target="_blank">G-Mo.R-Se</a> - G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads. From CNS in France.<br /> * <a href="http://evolution.sysu.edu.cn/english/software/mapnext.htm" target="_blank">MapNext</a> - MapNext: A software tool for spliced and unspliced alignments and SNP detection of short sequence reads. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China.<br /> * <a href="http://www.fml.tuebingen.mpg.de/raetsch/suppl/qpalma" target="_blank">QPalma</a> - Optimal Spliced Alignments of Short Sequence Reads. Authors are Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, and Gunnar R&auml;tsch. A paper is <a href="http://www.fml.tuebingen.mpg.de/raetsch/suppl/qpalma/qpalma-final.pdf" target="_blank">available</a>.<br /> * <a href="http://biogibbs.stanford.edu/%7Ejiangh/rsat/" target="_blank">RSAT</a> - RSAT: RNA-Seq Analysis Tools. RNASAT is developed and maintained by Hui Jiang at Stanford University.<br /> * <a href="http://tophat.cbcb.umd.edu/" target="_blank">TopHat</a> - TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland and the University of California, Berkeley</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/22961/bioscripts</guid>
	<pubDate>Sun, 28 Jun 2015 07:46:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/22961/bioscripts</link>
	<title><![CDATA[BioScripts]]></title>
	<description><![CDATA[<p>You are requested to please bookmark collection of bioinformatics tools, scripts, codes that can be pieced together in a very easy and flexible manner to perform both simple and complex bioinformatics tasks.</p>
<p>The next-generation sequencing included whole genome sequencing(WGS), transcriptome sequencing (whole cDNA sequencing, RNA-seq), digital gene expression sequencing (Tag-Seq), ChIP-Seq, and so on. And there are many sequencing platform to generate sequece, as well know Sanger/ABi(the frist generation), Solexa/illumina, SOLiD/ABi, 454/Roche. But thier sequence format is different, also they have different error type. High quality data is very important for further analysis or data mining. There are many pipeline for raw sequence quality analysis and control with few of process for reporting reads quality statistical details, trimming, filtering, and error correction. Please bookmarks them for the benefits of bioinformatics community.</p>
<p>https://code.google.com/p/biowiki/</p>
<p>https://code.google.com/p/ngs-pipeline/source/browse/#svn%2Ftrunk</p>
<p>NGSand Perl scripts https://code.google.com/hosting/search?q=NGS+perl&amp;projectsearch=Search+projects</p>
<p>NGS and Python scripts https://code.google.com/hosting/search?q=NGS+Python&amp;projectsearch=Search+projects</p><p>Address of the bookmark: <a href="https://code.google.com/hosting/search?q=bioinformatics&amp;sa=Search" rel="nofollow">https://code.google.com/hosting/search?q=bioinformatics&amp;sa=Search</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/23209/bisr-jaipur</guid>
  <pubDate>Tue, 07 Jul 2015 23:12:26 -0500</pubDate>
  <link></link>
  <title><![CDATA[BISR Jaipur]]></title>
  <description><![CDATA[
<p>The Bioinformatics Centre at BISR has created an infrastructure for providing facilities to the users working in the field of Biological Sciences. The users of Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics Centre extensively. The centre has leased line Internet connection as well latest Bioinformatics software for sequence and structure analysis. The centre provides the following services:</p>

<p>    Bioinformatics supports to researchers<br />    Customized training in Bioinformatics for researchers and faculty members<br />    Support in Installing, implementing and maintaining software on computer.<br />    Create awareness for taking preventive measure against data security<br />    Organize workshops on thrust ares of Bioinformatics<br />    Research Training to students of Biotechnology and Bioinformatics </p>

<p>More at http://bioinfo.bisr.res.in/index.php</p>
]]></description>
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