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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32709?offset=1270</link>
	<atom:link href="https://bioinformaticsonline.com/related/32709?offset=1270" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42130/shaman-a-user-friendly-website-for-metataxonomic-analysis-from-raw-reads-to-statistical-analysis</guid>
	<pubDate>Mon, 17 Aug 2020 05:21:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42130/shaman-a-user-friendly-website-for-metataxonomic-analysis-from-raw-reads-to-statistical-analysis</link>
	<title><![CDATA[SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis]]></title>
	<description><![CDATA[<p><span>SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, &hellip;).</span><br><span>The bioinformatics treatment is based on Vsearch [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/27781170">Rognes 2016</a><span>] which showed to be both accurate and fast [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/26664811">Wescott 2015</a><span>].The statistical analysis is based on DESeq2 R package [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/20979621">Anders and Huber 2010</a><span>] which robustly identifies the differential abundant features as suggested in [</span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974642/">McMurdie and Holmes 2014</a><span>] and [</span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/">Jonsson2016</a><span>]. SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/25516281">Love 2014</a><span>].</span><br><span>SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and figures can be downloaded in several formats. A presentation about SHAMAN is available&nbsp;</span><a href="https://github.com/aghozlane/shaman/blob/master/www/shaman_presentation.pdf">here</a><span>&nbsp;and a poster&nbsp;</span><a href="https://github.com/aghozlane/shaman/blob/master/www/shaman_poster.pdf">here</a><span>.&nbsp;</span></p>
<p><span>More at&nbsp;<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4</a></span></p><p>Address of the bookmark: <a href="https://github.com/aghozlane/shaman" rel="nofollow">https://github.com/aghozlane/shaman</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/20439/interactive-market-intelligence</guid>
	<pubDate>Mon, 19 Jan 2015 08:20:38 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/20439/interactive-market-intelligence</link>
	<title><![CDATA[Interactive Market Intelligence]]></title>
	<description><![CDATA[<p>BioInformatics LLC, a premier research and advisory firm serving the life science industry, has launched groundbreaking, dynamic-data presentation platform, Interactive Market Intelligence&mdash; the only cloud-based market research analytics tool for the life science tools industry.<br /><br />Superior to traditional PDF and PowerPoint reports, Interactive Market Intelligence allows end-users to filter, create and export literally thousands of views of data &mdash; all easily obtainable from a set of core metrics that include market, brand, customer and workflow analytics in well-defined segments of the life science market.<br /><br />The Market for Real-Time PCR is the first in a series of topics to be explored using the Interactive Market Intelligence platform. The primary research analysis is based on a survey of 900+ international scientists performing qPCR in their laboratories.<br /><br />Key data findings from "The Market for Real-Time PCR": Global market for qPCR in 2015 is estimated to be $3.6B; The average growth in qPCR throughput is expected to be at 9.8% in 2015; 22% of respondents are highly likely to switch primary suppliers of qPCR products; 50% of respondents use pre-designed primer/probe sets.</p>]]></description>
	<dc:creator>Pranjali Yadav</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42946/aligngraph2-similar-genome-assisted-reassembly-pipeline-for-pacbio-long-reads</guid>
	<pubDate>Sun, 14 Mar 2021 09:42:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42946/aligngraph2-similar-genome-assisted-reassembly-pipeline-for-pacbio-long-reads</link>
	<title><![CDATA[AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads]]></title>
	<description><![CDATA[<p><span>AlignGraph2 is the second version of&nbsp;</span><a href="https://github.com/baoe/AlignGraph">AlignGraph</a><span>&nbsp;for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.</span></p>
<p><span>More at&nbsp;https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/6146772</span></p><p>Address of the bookmark: <a href="https://github.com/huangs001/AlignGraph2" rel="nofollow">https://github.com/huangs001/AlignGraph2</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21537/bioinformatics-project-fellow-at-institute-of-genomics-integrative-biology-new-delhi-delhi</guid>
  <pubDate>Wed, 11 Mar 2015 03:04:38 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Project Fellow at Institute of Genomics &amp; Integrative Biology  - New Delhi, Delhi]]></title>
  <description><![CDATA[
<p>Pay Scale: Rs. 16,000/- + 30 % HRA per month<br />Educational Requirements: M.Sc. in Bioinformatics with at least 55% marks Qualifications: Knowledge of Perl, R and other programming language or Database management or knowledge of pipelines to analyze NGS data or experience in scientific writing and good communication skills </p>

<p>Details will be available at: http://www.igib.res.in/sites/default/files/26032015.pdf </p>

<p>No of Post: 01, 01 </p>

<p>How To Apply: 1. Please fill up the proforma 2. Candidate cannot apply for more than two posts. Last date of receiving application is 12-03-2015. No application would be entertained with “result awaited” status or after due date. List of shortlisted candidates will be put up on CSIR-IGIB website. No TA/DA will be paid to the candidates to attend the interview. The engagement shall be as per guidelines of CSIR/Funding agency. Candidates will have an option to give reply in Hindi. Note: The shortlisted candidates, have to report at 09:00 AM at Mall Road Campus, Delhi – 110007 on the day of interview along with any Photo ID card, (without photo ID card interview will not be conducted). 3 copies of updated signed C. V. (clearly mentioning Date of Birth and Hightest Qualification with percentage), Dissertation (if any), PhD thesis (if any) and original certificates/Self attested photocopies for verification. </p>

<p>General Instructions: Engagement is for the project and on behalf of the funding agency and the tenure shall be as mentioned above. The duration of the post is initially for One year or till the closing date of the project, whichever is earlier. Tenure may be extendable up to project duration. Contract may be terminated at any time by giving one-month notice by either side. The applicants will have no claim implicit or explicit for consideration against any CSIR/IGIB post. Candidates should note that non-fulfillment of the eligibility criterion will result in cancellation of candidature at any stage. </p>

<p>Last Date: 12-03-2015. <br />Age Limit: 28 Years</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44234/steps-to-find-palindrome-in-genomes</guid>
	<pubDate>Thu, 09 Mar 2023 02:56:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44234/steps-to-find-palindrome-in-genomes</link>
	<title><![CDATA[Steps to find palindrome in genomes !]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Palindromes are sequences of nucleotides that read the same backward as forward. They can be present in genomes and have various biological functions. Here are some methods for discovering palindromes in genomes:</p><ol>
<li>
<p>Direct sequence search: One of the simplest ways to discover palindromes is to search the genome sequence directly for palindromic sequences using pattern matching tools, such as regular expressions or string algorithms. This approach can be useful for discovering simple palindromes, but may miss more complex palindromic structures.</p>
</li>
<li>
<p>Dot plot analysis: Dot plot analysis is a graphical method that can be used to identify palindromic regions in a genome. It involves plotting the genome sequence against itself and examining the diagonal patterns that emerge. Palindromic regions will appear as symmetrical patterns along the diagonal.</p>
</li>
<li>
<p>Restriction enzyme analysis: Some restriction enzymes, such as EcoRI and HindIII, recognize palindromic sequences and cleave DNA at these sites. By digesting the genome with these enzymes and examining the resulting fragments, palindromic regions can be identified.</p>
</li>
<li>
<p>Next-generation sequencing: High-throughput sequencing technologies, such as PacBio and Oxford Nanopore, can generate long reads that can span entire palindromic regions. By mapping these reads to the genome, palindromic regions can be identified and characterized.</p>
</li>
<li>
<p>Comparative genomics: Comparing the genomes of related species can also reveal palindromic regions that are conserved across evolutionarily divergent lineages. This approach can help identify functional palindromes that are under selective pressure.</p>
</li>
</ol><p>Overall, the discovery of palindromic sequences in genomes can be accomplished using a variety of methods, each with their own advantages and limitations. A combination of these methods can provide a comprehensive understanding of the palindromic landscape of a genome.</p></div></div></div></div></div></div></div></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/33617/list-of-universities-offering-bachelor-or-master-bioinformatics-degree-in-pakistan</guid>
	<pubDate>Wed, 21 Jun 2017 04:20:43 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/33617/list-of-universities-offering-bachelor-or-master-bioinformatics-degree-in-pakistan</link>
	<title><![CDATA[List of universities offering Bachelor or Master bioinformatics degree in Pakistan]]></title>
	<description><![CDATA[<p>There are a lot of universities offering Bachelor or Master degree in Pakistan. Following are the list of few intitute/universities</p><p>Bachelor/ BS Bioinformatics at<br />1. Al-khair University, Bhimber<br />2. Government College University, Faisalabad<br />3. University Of Agriculture, Faisalabad<br />4. Comsats Institute Of Information Technology [isb], Islamabad<br />5. International Islamic University, Islamabad<br />6. Quaid-e-azam University, Islamabad<br />7. Khushal Khan Khattak University, Karak<br />8. Virtual University Of Pakistan, Lahore<br />9. Virtual University Of Pakistan, Lahore<br />10. Hazara University, Mansehra<br />11. Shaheed Benazir Bhutto Women University, Peshawar<br />12. Comsats Institute Of Information Technology, Sahiwal<br />13. Capital University Of Science And Technology, Islamabad<br />14. Foundation University, Islamabad<br />15. Baqai Medical University/hospital, Karachi<br />16. Institute Of Business And Technology(main Campus), Karachi<br />17. Sir Syed University Of Engineering &amp; Technology, Karachi<br />18. Forman Christian College, Lahore<br />19. Qarshi University (lhr), Lahore<br />20. The Superior University, Lahore<br />21. University Of Management And Technology, Lahore<br />22. Federal Institute Of Health Sciences, Lahore<br />23. Shaheed Benazir Bhutto Women University Peshawar, Sub Campus, Swabi<br />24. Government Postgraduate College ( Mandian), Abbottabad<br />25. Federal Institute Of Health Sciences, Multan<br />26. Fedral Institute Of Health Sciences, Muzaffarabad<br />27. The Limit Institution Of Health Sciences, Sahiwal</p><p><br />Master/ MS Bioinformatics cources at<br />1. Government College University, Faisalabad<br />2. Comsats Institute Of Information Technology [isb], Islamabad<br />3. International Islamic University, Islamabad<br />4. National University Of Science &amp; Technology, Islamabad<br />5. Quaid-e-azam University, Islamabad<br />6. University Of Sindh, Jamshoro<br />7. Virtual University Of Pakistan, Lahore<br />8. Hazara University, Mansehra<br />9. Shaheed Benazir Bhutto Women University, Peshawar<br />10. Capital University Of Science And Technology, Islamabad<br />11. Cecos University Of Information Tech. &amp; Emerging Sciences, Peshawar</p><p>The real bioinformatics scope lies if there are research labs which work in this field. One has to take account of that. If so then try to get information of those labs and visit them to get a hang of the work they pursue.</p><p>There is a huge buzz of precision medicine in light of genomics all around the world. One should also try to see how genomics infrastructure is built up or standing in Pakistan. If research labs having collaboration with hospitals employ genomics then one must also visit such labs. This will bring new avenues in healthcare advances. Not only it opens up the wealth of knowledge one can make out of genomics study but will also advance the critical thinking of therapies.</p><p>So I would encourage to target research labs working in the fields and also get information of hospitals employing genomics, this will give you an overall understanding of the fields demand in your country.</p>]]></description>
	<dc:creator>Reshma Khatun</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38563/hecil-a-hybrid-error-correction-algorithm-for-long-reads-with-iterative-learning</guid>
	<pubDate>Tue, 01 Jan 2019 12:01:00 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38563/hecil-a-hybrid-error-correction-algorithm-for-long-reads-with-iterative-learning</link>
	<title><![CDATA[HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning]]></title>
	<description><![CDATA[<p><span>HECIL&mdash;Hybrid Error Correction with Iterative Learning&mdash;a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read alignments.&nbsp;</span></p>
<p><span><span>HECIL&rsquo;s core algorithm by introducing an iterative learning paradigm that enhances the correction policy at each iteration by incorporating knowledge gathered from previous iterations via data-driven confidence metrics assigned to prior corrections.</span></span></p><p>Address of the bookmark: <a href="https://github.com/NDBL/HECIL" rel="nofollow">https://github.com/NDBL/HECIL</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/23537/research-associate-bioinformatics-central-institute-for-research-on-buffaloes-cirb-hisar-haryana</guid>
  <pubDate>Fri, 31 Jul 2015 10:19:45 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate Bioinformatics Central Institute for Research on Buffaloes (CIRB) - Hisar, Haryana]]></title>
  <description><![CDATA[
<p>Research Associate (RA) under Network Project on Agricultural Bioinformatics</p>

<p>Name of the Project : Network Project on Agricultural Bioinformatics Number of positions One<br />Qualifications : Ph.D Degree in Bioinformatics/Biotechnology/ Biochemistry/Genetics &amp; Breeding/Life Sciences OR Master’s Degree in relevant subject with at least 2 years research experience. Desirable : Working experience in Molecular Biology/Genomics/Bioinformatics, specifically, sequence data analysis using software’s proficiently</p>

<p>Emoluments : Masters Degree Holders Rs. 38,000/- per month Doctoral Degree Holders Rs. 40,000/- per month</p>

<p>Emoluments : Rs.25000/- per month for 1st and 2nd year and Rs. 28000/- per month for 3rd year<br />Age Limit : Upper age limit is 35 years for men and 40 years for women on the date of interview. Age relaxation for SC/ST and OBC candidates as per rules</p>

<p>More at http://www.cirb.res.in/attachments/195_walk-in-interview%20for%20contractual%20positions%20of%20RA%20and%20SRF%20%28On%20Dated%2011.8.2015%29.pdf</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21022/ra-bioinformatics-at-tezpur-university</guid>
  <pubDate>Fri, 06 Feb 2015 04:11:23 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at TEZPUR UNIVERSITY]]></title>
  <description><![CDATA[
<p>Walk-in-interview will be held on 23 February, 2015 at 11.00 a.m. for the following temporary positions in the DBT (U-EXCEL) sponsored project entitled “Sequencing genomes of some bacteria that invade/resides in tomato plant” under the Principal Investigator Dr. Suvendra Kumar Ray, Department of Molecular Biology and Biotechnology, Tezpur University.</p>

<p>Interested candidates may appear before the interview board on 23 February, 2015 at the Office of the Head, Department of Molecular Biology &amp; Biotechnology, Tezpur University with original documents and photocopies of marks sheets, certificates, testimonials, caste certificate (if applicable), experience certificate and a copy of curriculum vitae (CV) duly signed by the candidate.</p>

<p>Position: One (01) Research Associate.</p>

<p>Educational Qualification: Candidates having Ph.D. degree or submitted thesis in any topic of Life Science Areas (Zoology, Botany, Microbiology, Biotechnology etc.) along with knowledge of gene and protein sequence analysis may apply.</p>

<p>Remuneration: Rs. 22,000/- (Rupees twenty two thousand) only + 10% HRA as admissible per month for the first year and Rs. 23,000/- (Rupees twenty three thousand) only + 10% HRA as admissible per month for the second year.</p>

<p>Age: Candidate preferably below the age of 40 years who have obtained a doctorate (Ph.D.) degree from a recognized University.</p>

<p>Upper age limit may be relaxed up to 5 years in the case of candidates belonging SC/ST/OBC/Women and physically challenged.</p>

<p>Position: One (01) Project Assistant.</p>

<p>Educational Qualification: B.Sc./B.Tech./B.E./B.Pharma in any branch with minimum 55% mark in the qualifying examinations and minimum 50 % mark in 10th and 10+2 Science examinations.</p>

<p>Remuneration: Rs. 8,000/- (Rupees eight thousand) only per month (consolidated). Age: Candidate should not be more than 28 years of age on the date of interview. Upper age limit may be relaxed up to 5 years in the case of candidate belonging to SC/ST/OBC/Women/Physically Challenged.</p>

<p>Duration: One year or till completion of the project, whichever is earlier. N.B. No TA/DA will be paid to the candidates for attending the interview.</p>

<p>For further information contact – Dr. Suvendra Kumar Ray, Associate Professor Email: suven@tezu.ernet.in Department of Molecular Biology and Biotechnology Tezpur University Sd/- Dean, Research &amp; Development Tezpur University</p>

<p>Advertisement: http://www.tezu.ernet.in/ProjectWalkin/Advt-SKR2-5342-A.pdf</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21095/ra-walk-in-interview-actrec</guid>
  <pubDate>Mon, 09 Feb 2015 01:06:16 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA WALK-IN-INTERVIEW @ ACTREC]]></title>
  <description><![CDATA[
<p>No. ACTREC/Advt./ 7 /2015</p>

<p>Title of the Project<br />Research Associate<br />(One position)<br />DBTs Biotechnology/Bioinformatics training centre<br />PI Dr. Ashok Varma	</p>

<p>Duration of the Project Six Months from the date of appointment, can be extended further for six month.</p>

<p>Date &amp; Time: 17th February, 2015 at 10.00 a.m.</p>

<p>Venue: Meeting Room, 3rd floor, Khanolkar Shodhika, ACTREC</p>

<p>Essential Qualifications and Experience:</p>

<p>Ph.D. Degree in Basic Sciences from recognized University. Research experience in Bioinformatics or on gene cloning, protein purification, and crystallization.</p>

<p>*M.Sc. degree obtained after a one year course will not be considered.</p>

<p>Selected candidate will have to join at the earliest.</p>

<p>Consolidated Salary: Rs.28,600/- p.m. {Rs.22,000/- + 30% HRA}</p>

<p>The work progress of the candidate will be monitored and extension after 6 months will depend on satisfactory progress of the work.</p>

<p>Candidates fulfilling these requirements should pre-register by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to ‘program.office@actrec.gov.in’ latest by 17.00 hrs on 12-02-2015.<br />The interviews would be held on 17th February, 2015 and will be only for the pre-registered candidates. Candidates should report between 09.30 to 10.00 a.m. in Steno Pool, 3rd floor, Khanolkar Shodhika, ACTREC, Kharghar, Navi Mumbai.<br />No T.A./D.A. will be admissible for attending the interview.</p>

<p>At the time of Interview the candidate should bring original certificates along with CV with contact details of 2 referees and submit the photocopies (attested) of the certificates, with a recent passport size photograph.</p>

<p>All correspondence should be strictly made only to ‘program.office@actrec.gov.in’ as indicated.</p>

<p>Advertisement: www.actrec.gov.in/data%20files/2015/AV-RA-DBT-28-1-15.docx</p>
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