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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/22050?offset=70</link>
	<atom:link href="https://bioinformaticsonline.com/related/22050?offset=70" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21435/ra-walk-in-interview-nbfgr-lucknow</guid>
  <pubDate>Tue, 24 Feb 2015 08:23:48 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA WALK-IN-INTERVIEW @ NBFGR, Lucknow]]></title>
  <description><![CDATA[
<p>F.No. 1(122)/2015-Admn. (CABin Project)<br />Research Associate/Young Professional/SRF Zoology job vacancies in National Bureau of Fish Genetic Resources (NBFGR)<br />Post Name: Research Associate (Computer Science/ Applications)                <br />Qualification: Ph.D. In Computer Science/Computer Applications or equivalent. Or Post-Graduation in Computer Science/ Computer Applications with 1st Division or 60% marks or equivalent overall grade point average with at least two years of research experience. Desirable: 1. Expertise and experience of working/ handling High Performance Computing (H PC) and genomic resource data. 2. Expertise on database management, data mining technologies/ softwares/tools. 3. Published Research papers	<br />No.of Post: 1<br />Pay Scale: Consolidated Rs.24,000/- p.m. + HRA (as admissible) for Ph.D. holders and consolidated `23,000/- + HRA (as admissible) for Master degree holder.	<br />Age:40 years</p>

<p>Young Professional II (Computer Science/Applications)	<br />Master degree in Computer Science/Computer Applications/B.Tech (Computer Science) or equivalent. <br />Desirable: 1. Knowledge of Statistical and Computational Genomics/ Proteomics/ Bioinformatics/Data mining tools. 2. Experience in handling HPC, programming languages and database management packages.	<br />A consolidated salary of Rs.25,000/- per month.	<br />21 to 45 year</p>

<p>Young Professional II (Biotechnology/ Bioinformatics)	<br />Master degree in Bioinformatics/ Biotechnology/ B. Tech(Biotech) or equivalent. Desirable: 1. Knowledge of Computational Genomics/Proteomics/Bioinformatics. 2. Expertise in NGS data analysis and knowledge of allied software and tools.	<br />A consolidated salary of Rs.25,000/- per month.	</p>

<p>Senior Research Fellow	<br />1. Bachelors degree with Zoology, Fisheries and 2. Master's degree in Fishery science/ Zoology with Fisheries/ Biotechnology/ Life Sciences with specialization in Fisheries/ Molecular Biology. 3. 1 st Division or 60% marks or equivalent overall grade point average. <br />Desirable: Work experience in Fisheries, molecular research techniques, bioinformatics and Computer skills. NET qualified <br />Note: The project involves extensive exploration tours and sampling from water bodies all over India	<br />Rs.16,000/- p.m. for 1st &amp; 2nd year and `18,000/- p.m. for 3rd and subsequent years +HRA (as per rules)	35 years for male and 40 years for female candidate</p>

<p>How to apply</p>

<p>A walk-in-interview will be held on 04th March, 2015 at 10:00 hrs at National Bureau of Fish Genetic Resources, Lucknow. Eligible and desirous candidates fulfilling all the requirements may appear for the interview with duly filled in application giving full details of academic records and experience(s) along with attested photocopy as well as original copy of the relevant documents and a passport size photograph on the attached proforma.</p>

<p>http://www.nbfgr.res.in/</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/21443/a-guide-for-complete-r-beginners-getting-data-into-r</guid>
	<pubDate>Tue, 24 Feb 2015 20:15:08 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/21443/a-guide-for-complete-r-beginners-getting-data-into-r</link>
	<title><![CDATA[A guide for complete R beginners :- Getting data into R]]></title>
	<description><![CDATA[<p>For a beginner this can be is the hardest part, it is also the most important to get right.</p><p>It is possible to create a vector by typing data directly into R using the combine function &lsquo;c&rsquo;</p><blockquote><p><strong>x </strong></p></blockquote><p>same as</p><blockquote><p><strong>x </strong></p></blockquote><p>creates the vector x with the numbers between 1 and 5.</p><p>You can see what is in an object at any time by typing its name;</p><blockquote><p><strong>x</strong></p></blockquote><p>will produce the output<strong> &lsquo;[1] 1 2 3 4 5&prime;</strong></p><p>Note that names need to be quoted</p><blockquote><p><strong>daysofweek </strong><strong>&larr; c(&lsquo;Monday&rsquo;, &lsquo;Tuesday&rsquo;, &lsquo;Wednesday&rsquo;, &lsquo;Thursday&rsquo;, &lsquo;Friday&rsquo;);</strong></p></blockquote><p>Usually however you want to input from a file. We have touched on the &lsquo;read.table&rsquo; function already.</p><blockquote><p><strong>mydata </strong></p></blockquote><p>Now <strong>mydata</strong> is a data frame with multiple vectors</p><p>each vector can be identified by the default syntax</p><p>#if any of these are typed it will print to screen</p><blockquote><p><strong>mydata$V1 mydata$V2 mydata$V3 </strong></p></blockquote><p>By default the function assumes certain things from the file</p><ul>
<li>The file is a plain text file (there are function to read excel files: <em>not covered here</em>)</li>
<li>columns are separated by any number of tabs or spaces</li>
<li>there is the same number of data points in each column</li>
<li>there is no header row (labels for the columns)</li>
<li>there is no column with names for the rows** [I&rsquo;ll explain].</li>
</ul><p><span style="text-decoration: underline;">If any of these are false, we need to tell that to the function</span></p><p>If it has a header column</p><blockquote><p><strong>mydata <em>header=T also works</em></strong></p></blockquote><p>Note that there is a comma between different parts of the functions arguments</p><p>If there is one less column in the header row, then R assumes that the 1<sup>st</sup> column of data after the header are the row names</p><p>Now the vectors (columns) are identified by their name</p><p>#if any of these are typed it will print to screen</p><blockquote><p><strong>mydata$A mydata$B mydata$C </strong></p></blockquote><p># Summary about the whole data frame</p><blockquote><p><strong>summary(mydata)</strong></p></blockquote><p># Summary information of column A</p><blockquote><p><strong>summary(mydata$A) </strong></p></blockquote><p>We can shortcut having to type the data frame each time by attaching it</p><blockquote><p><strong>attach(mydata)</strong></p></blockquote><p># summary of column B as &lsquo;mydata&rsquo; is attached</p><blockquote><p><strong>summary(B)</strong></p></blockquote><p><span style="text-decoration: underline;">Two other important options for </span><em><span style="text-decoration: underline;">read.table</span></em></p><p>If is is separated only by tabs and has a header</p><blockquote><p><strong>mydata </strong></p></blockquote><p>Really useful if you have spaces in the contents of some columns, so R does not mess up reading the columns . However if the columns or of an uneven length it will tell you.</p><p>If you know that the file has uneven columns</p><blockquote><p><strong>mydata </strong></p></blockquote><p>This causes R to fill empty spaces in a columns with &lsquo;NA&rsquo; .</p><p>The last two examples will still work with our file and give the same result as with only headers=T</p><p><span style="text-decoration: underline;">Graphs</span></p><p>to get an idea of what R is capable of type</p><blockquote><p><strong>demo(graphics)</strong></p></blockquote><p>steps through the examples, and the code is printed to the screen</p><p>We will work with simpler examples that have immediate use to biologists.</p><p>Remember to get more information about the options to a function type &lsquo;?function&rsquo;</p><p><span style="text-decoration: underline;">Histogram of A</span><span style="text-decoration: underline;"></span></p><blockquote><p><strong>hist(mydata$A)</strong></p></blockquote><p>If there was more data we could increase the number of vertical columns with the option, breaks=50 (or another relevant number).</p><blockquote><p><strong>boxplot(mydata)</strong></p></blockquote><p>We can get rid of the need to type the data frame each time by using the <strong>attach</strong> function</p><p># if not already done so</p><blockquote><p><strong>attach(mydata) </strong></p><p><strong>boxplot(mydata$A, mydata$B, name=c(&ldquo;Value A&rdquo;, &ldquo;Value B&rdquo;) , ylab=&ldquo;Count of Something&rdquo;)</strong></p></blockquote><p>same as</p><blockquote><p><strong>boxplot(A, B, name=c(&ldquo;Value A&rdquo;, &ldquo;Value B&rdquo;) , ylab=&ldquo;Count of Something&rdquo;)</strong></p></blockquote><p><span style="text-decoration: underline;">Scatter plot</span></p><p># if not already done so</p><blockquote><p><strong>attach(mydata) </strong></p><p><strong>plot(A,B) # or plot(mydata$A, mydata$B)</strong></p></blockquote><p><strong><span style="text-decoration: underline;">SAVING an image</span></strong></p><p>Windows users (Rgui) RIGHT click on image and select which you want.</p><p><span style="text-decoration: underline;">These instructions work for everyone.</span></p><p>You need to create a new device of the type of file you need, then send the data to that device</p><p>to save as a png file (easy to load into the likes of powerpoint, also great for web applications.</p><blockquote><p><strong>png(&lsquo;filename&rsquo;) </strong></p><p><strong>boxplot(A, B, name=c(&ldquo;Value A&rdquo;, &ldquo;Value B&rdquo;) , ylab=&ldquo;Count of Something&rdquo;)</strong></p></blockquote><p>or to save as a pdf</p><blockquote><p><strong>pdf(&lsquo;filename&rsquo;) </strong></p><p><strong>boxplot(A, B, name=c(&ldquo;Value A&rdquo;, &ldquo;Value B&rdquo;) , ylab=&ldquo;Count of Something&rdquo;)</strong></p></blockquote><p><span style="text-decoration: underline;">Note</span></p><ul>
<li>Nothing will appear on screen, the output is going to the file</li>
<li>Also it may not be saved immediately but will once the device (or R) is turned quit.</li>
</ul><p>To quit R type</p><p><strong>q() # </strong>If you save your session, next time you start R, you will have your data preloaded.</p><p>Or if you want to remain in R</p><blockquote><pre><strong>dev.off() #</strong>turns of the png (or pdf etc) device, thus forces the data to save</pre></blockquote>]]></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/opportunity/view/21934/ra-bioinformatics-at-bose-institute</guid>
  <pubDate>Tue, 07 Apr 2015 03:30:25 -0500</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at Bose Institute]]></title>
  <description><![CDATA[
<p>Bose Institute, Kolkata, invites online applications from Indian Citizens for recruitment of Research Associate (05 posts) under Institute Plan Programmes : Improvement of Plants : Biotechnological, Genomic and Proteomic Approaches (programme No. – I), Bioinformatics and Computational Biology (programme No. – III), Microbial Genomics and Infection Biology (programme No. – V) and Basic &amp; Applied Problems in Physical and Environmental Sciences (programme No. – VII). All the posts are tenable for one (01) year.</p>

<p>ESSENTIAL QUALIFICATION: PH.D. DEGREE IN LIFE SCIENCES / PHYSICAL SCIENCE.</p>

<p>Research Associate for Programme No. –I Specialization in the area of plant molecular biology or plant proteomic study or plant pathogen interaction.<br />Research Associate for Programme No. –I Specialization in the area of plant / fungal Biotechnology, tissue culture and molecular biology<br />Research Associate for Programme No. –III Specialization in the area of structural biology and protein crystallography.<br />Research Associate for Programme No. – V Specialization in the area of microbial physiology (metabolism) or environmental microbiology, with experience in microbial genomics and proteomics.<br />Research Associate for Programme No. – VII Specialization in the area of Theoretical High Energy Astrophysics or Astroparticle Physics. Proven record of independent research experience in Astrophysical<br />Radiation Magnetohydrodynamics or Cosmic Ray Astrophysics. Experience in numerical techniques and /or date analysis would be additional advantage.<br />Associateship : 22,000/- p.m., plus admissible H.R.A. and Medical benefit.<br />Age: Below 3 Age : Below 35 years (Relaxable in case of SC/ST/OBC/Women candidates only as per rule).<br />SELECTION PROCEDURE FOR BOSE INSTITUTE- RESEARCH ASSOCIATE POST:</p>

<p>Candidates can apply on or before 13/4/2015.<br />No detailed information about the selection procedure is mentioned in the recruitment notification.<br />HOW TO APPLY FOR RESEARCH ASSOCIATE VACANCY IN BOSE INSTITUTE:</p>

<p>Interested and eligible candidates may read the application procedures and instructions carefully before applying through online as well as submitting the hard copy of the same. Candidates those who has submitted their Ph.D. Thesis and can produce Provisional Ph.D. Certificate at the time of Interview may also apply </p>

<p>Ref<br />Bose Institute Recruitment 2015 –  ADVT. NO. : BI/IF/35/2014-15.</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22072/bioinformatics-jrfrasrf-position-at-indian-institute-of-science-education-and-research-iiser-kolkata-kolkata-west-bengal</guid>
  <pubDate>Fri, 17 Apr 2015 04:11:14 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics JRF/RA/SRF position at Indian Institute of Science Education and Research (IISER Kolkata) - Kolkata, West Bengal]]></title>
  <description><![CDATA[
<p>Research Position in Computational Biology in the group of Shree P. Pandey Positions available in the area of NGS data analysis, bioinformatics, plant genomics</p>

<p>Project Description: Projects involves high throughput analysis of data mostly generated by massively parallel sequencing (RNA-Seq and small-RNA-Seq), microarrays and related platforms. We are looking for highly motivated and bright individuals interested in high-throughput cutting-edge data analyses methods in genomics (computational positions). Available positions: Applications are invited from suitable candidates in both, the Max Planck India Partner Program and the CRP Wheat Program for openings at the levels:</p>

<p>Post Name-Qualification-Salary:<br />Project assistant – Master’s – Rs. 14000<br />Project fellow (junior data analyst) – Masters + research experience – Rs. 16000<br />Research fellow (senior data analyst) – Masters + adequate research experience/desirable skill sets – Rs. 22000<br />Research Associated – PhD (&lt; 1yr) /&gt; 1 yr experience – Rs. 28000 / Rs. 32000<br />Essential qualification: MSc/MTech/PhD (or other suitable qualification) in discipline related to bioinformatics, computational biology, computer application (or equivalent)/ ‘Advance Post-Graduate Diploma in Bioinformatics’. Proficiency in one of the programming languages or statistics (proficient in R for example) is compulsory.<br />Desirable qualification: 1. Programming experiences in at least one low level language such as C/C++ and one scripting language such as Perl/Python/PHP and knowledge of SQL/MySQL. 2. Substantial experience in the linux or other unix environments. 3. Experience of working in projects on Bioinformatics, Genetics or Biological application areas/Computational and Statistical analysis (e.g. using R or Matlab). Experience in the field of genomics (NGS, microarrays, genome annotation), database development and management, software development, systems and network biology (or related fields) will be preferred.<br />SELECTION PROCEDURE FOR INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH (IISER KOLKATA) – RESEARCH ASSOCIATE &amp; MORE VACANCIES POST:</p>

<p>Candidates can apply on or before 30/04/2015<br />No Detailed information about the selection process is mentioned in the recruitment notification<br />HOW TO APPLY FOR RESEARCH ASSOCIATE &amp; MORE VACANCIES IN INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH (IISER KOLKATA):</p>

<p>Applications should contain CV along with brief description (maximum 1 page) of research conducted (highlighting skills and experience) till now. Applications should be sent by email to Shree P. Pandey, Department of Biological Sciences, IISER-Kolkata, Mohanpur Campus, West Bengal within 2 weeks. Interviews will be scheduled within 10 days of closing of applications. E-mail: sppiiserkol@gmail.com, sppandey@iiserkol.ac.in<br />For more details visit: http://www.iiserkol.ac.in/~sppandey</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22235/project-fellow-bioinformatics-at-central-drug-research-institute</guid>
  <pubDate>Mon, 27 Apr 2015 20:15:45 -0500</pubDate>
  <link></link>
  <title><![CDATA[Project Fellow Bioinformatics at Central Drug Research Institute]]></title>
  <description><![CDATA[
<p>Project Fellow (Bioinformatics)<br />Central Drug Research Institute<br />Address: Chattar Manzil, M.G.Road, Kaisarbagh<br />Postal Code: 226001<br />City: Lucknow<br />State: Uttar Pradesh<br />Pay Scale: Rs.16,000/- (fixed) p.m.<br />Educational Requirements: M.Sc. in Bioinformatics with 55% marks for Gen. &amp; OBC and 50% marks for SC/ST candidates, Physically and Visually handicapped candidates<br />Experience Requirements: Experience in computer-assisted scientific research in the area of Drug Design including Bio- molecular modeling and simulation studies, Virtual screening, pharmacophore perception, QSAR etc. Familiarity with Linux/Unixbased computer systems and required to participate and contribute to the development and application of computational models for the design and discovery of novel molecules as inhibitors or chemical probes<br />Details will be available at: http://cdriindia.org/uploaded/advt_no01-2015.pdf</p>

<p>How To Apply: Eligible candidates required to report for the Interview at 9:00 A.M. sharp on 11-05-2015 (For Position Code No. 001 to 009) and 12-05-2015 (For Position Code No. 010 to 016). Candidates reporting after 10:00 A.M will not be allowed to attend the interview. Eligible candidates may appear before the Selection Committee for interview on the date and time mentioned above at CDRI, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow-226031. Eligible candidates must bring with them duly filled up application form (which can be downloaded from our website www.cdriindia.org), along with Original certificates as well as attested copies of certificates of examinations starting from matriculation, date of birth, caste certificate (in case of SC/ST/OBC) experience certificate, publication, if any and recent passport size photograph etc. Original documents are essential for verification of the particulars quoted by the candidate in the application form and candidate failed to produce original documents at the time of verification, shall not be allowed to attend the interview. Any request for relaxation in this regard shall not be entertained.<br />Detail of Interview: 11-05-2015<br />Age Limit: 28 Years</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22269/school-of-life-sciences-jawaharlal-nehru-university-vacancy-of-jrf-srf-ra-in-csir-funded-project</guid>
  <pubDate>Wed, 29 Apr 2015 21:26:19 -0500</pubDate>
  <link></link>
  <title><![CDATA[School of Life Sciences, Jawaharlal Nehru University vacancy of JRF / SRF / RA in CSIR funded Project]]></title>
  <description><![CDATA[
<p>School of Life Sciences, Jawaharlal Nehru University has issued notification dated 27.04.2015 to fill the vacancy of JRF / SRF / RA in CSIR funded Projec entitled "Structural and functional characterization of serine biosynthetic pathway enzymes from entamoeba histolytica". It is good chance to get job with IITKGP and brighten your future. Learn eligibility criteria and apply on or before 08.05.2015.</p>

<p>Employer:	Jawaharlal Nehru University<br />Address:	Dr. S. Gourinath, Principal Investigator, School Of Life Sciences, Jawaharlal Nehru University, New Delhi-110067<br />Email:	not mentioned / provided for this job post<br />URL:	http://www.jnu.ac.in/Career/currentjobs.htm<br />Phone:	011 2674 2575<br />Skills:	not mentioned / required for this job post<br />Experience:	Experience in molecular biology, structural biology and bioinformatics is desired<br />Education:	M.Sc. in any field of life sciences.<br />Job Location:	New Delhi, Delhi, India   (View Jobs in New Delhi,   Jobs in Delhi,   Jobs in India)</p>

<p>Job Description: School of Life Sciences, Jawaharlal Nehru University vacancy of JRF / SRF / RA in CSIR funded Projec</p>

<p>Name of the Post: JRF / SRF / RA</p>

<p>Salary: As per rules</p>

<p>Required Job Profile:</p>

<p>Candidate must possess M.Sc. in any field of life sciences.</p>

<p>Desired Job Profile:</p>

<p>Candidate having NET - CSIR or UGC and experience in molecular biology, structural biology and bioinformatics is desired and experience with publication is preferred.</p>

<p>How to apply:</p>

<p>Eligible and interested candidates should need to apply with complete details to the above mentioned address on or before 08.05.2015.</p>

<p>Refer to http://www.jnu.ac.in/Career/currentjobs.htm</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22437/jrf-bioinformatics-icar-national-research-centre-for-orchids-pakyong</guid>
  <pubDate>Thu, 28 May 2015 19:33:19 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF Bioinformatics @ ICAR - National Research Centre for Orchids  Pakyong]]></title>
  <description><![CDATA[
<p>ICAR - National Research Centre for Orchids</p>

<p>Pakyong</p>

<p>F.No:NRCO/Admn/DBT /136 /</p>

<p>Walk-in-Interviews will be held at 737106, Sikkim for the post of 01 (One Project ‘DBT’s Twinning programme for the NE’ titled “Assessment of some fragrant orchids of north-east India for sustainable improvement of community livelihood”, indicated below. The appointment will be on contractual basis and the incumbents shall not have any regular appointment in ICAR.</p>

<p>‘DBT’s Twinning programme for the NE’ titled “Assessment of chemical and genetic divergence of some fragrant orchids of north-east India for sustainable improvement of community livelihood”</p>

<p>Junior Research Fellow (One post)</p>

<p>Essential Qualification : a. MSc (with NET qualification) / M.Tech degree (with or without NET) with minimum 55% marks in Biotechnology/ Bioinformatics/ Molecular Biology or any other related field.</p>

<p>Desirable Qualification: Computer Skills (Linux, Perl, Java, MySQL) with experience in advanced molecular Biology techniques</p>

<p>2nd June 2015</p>

<p>Advertisement: www.nrcorchids.nic.in/Employments/Vacancy%20-%20JRF.pdf</p>
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	<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/opportunity/view/22786/ra-at-university-of-delhi</guid>
  <pubDate>Wed, 17 Jun 2015 20:35:35 -0500</pubDate>
  <link></link>
  <title><![CDATA[RA at University of Delhi]]></title>
  <description><![CDATA[
<p>Research Scientist Jobs opportunity in University of Delhi on temporary basis</p>

<p>Qualifications : Ph. D.</p>

<p>Desirable : Experience on DNA Markers, plant genome mapping and bioinformatics</p>

<p>No. of Post : 03</p>

<p>Department : Genetics</p>

<p>Salary : Rs. 60,000/-<br />How to apply</p>

<p>The applicants are requested to register their names on the day of interview in the First Floor, Biotech Centre, Centre for Genetic Manipulation of Crop Plants, Department of Genetics before the stipulated time for the interview. Only the registered eligible candidates will be interviewed on the day in the Committee Room. Applicants are requested to bring all related documents, in original and a set of photocopy, for verification. Date and time of the interview : 25.06.2015 at 10:30 AM.</p>

<p>Click Here for Job Details http://www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&amp;cntnt01articleid=5492&amp;cntnt01returnid=83</p>
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