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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/31087?offset=750</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36800/genomemapper-simultaneous-alignment-of-short-reads-against-multiple-genomes</guid>
	<pubDate>Fri, 25 May 2018 09:29:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36800/genomemapper-simultaneous-alignment-of-short-reads-against-multiple-genomes</link>
	<title><![CDATA[GenomeMapper: Simultaneous alignment of short reads against multiple genomes]]></title>
	<description><![CDATA[GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use the latter

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768987/<p>Address of the bookmark: <a href="http://1001genomes.org/software/genomemapper.html" rel="nofollow">http://1001genomes.org/software/genomemapper.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25409/jrf-bioinformatics-at-cuk</guid>
  <pubDate>Thu, 03 Dec 2015 23:40:38 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF Bioinformatics at CUK]]></title>
  <description><![CDATA[
<p>JRF Bioinformatics</p>

<p>Eligibility : MSc(Bio-Informatics), BE/B.Tech</p>

<p>Location : Kasaragod</p>

<p>Last Date : 20 Dec 2015</p>

<p>Hiring Process : Face to Face Interview<br />Central University of Kerala</p>

<p>JRF job opportunity in Central University of Kerala (CUK) on temporary basis </p>

<p>Project Title : "Targeting TAL effector mediated susceptibility for durable and broad-spectrum resistance to bacterial blight in Rice"</p>

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

<p>Qualification : MSc in any subject under Life Science or Bioinformatics/ B.Tech in Bioinformatics + 1 yr experience </p>

<p>Stipend : Rs. 14,000/-<br />How to apply</p>

<p>Interested candidates are requested to send their applications explaining their interest in the position with an updated CV to Dr. Ginny Antony, Assistant Professor, Department of Plant Science, School of Biological Sciences, Central University of Kerala, Padannakkad, Kasaragod, Kerala - 671 314 email: ginnycuk2013@gmail.com on or before 20th December, 2015.</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37502/alignqc-a-tool-for-assessing-an-alignment-and-generating-reports-that-are-easy-to-share</guid>
	<pubDate>Tue, 07 Aug 2018 04:41:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37502/alignqc-a-tool-for-assessing-an-alignment-and-generating-reports-that-are-easy-to-share</link>
	<title><![CDATA[AlignQC: A tool for assessing an alignment, and generating reports that are easy to share]]></title>
	<description><![CDATA[<p><span>Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.</span></p>
<p>https://f1000research.com/articles/6-100/</p>
<p>https://github.com/jason-weirather/AlignQC</p><p>Address of the bookmark: <a href="https://www.healthcare.uiowa.edu/labs/au/AlignQC/" rel="nofollow">https://www.healthcare.uiowa.edu/labs/au/AlignQC/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25651/jrftraineeshipstudentship-bioinformatics</guid>
  <pubDate>Thu, 10 Dec 2015 13:49:56 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF/Traineeship/Studentship Bioinformatics]]></title>
  <description><![CDATA[
<p>JRF/Traineeship/Studentship Bioinformatics</p>

<p>Eligibility : ME/M.Tech(Bio-Informatics/Bio-Chemistry Engg, CSE), MSc(Bio-Informatics, CS)</p>

<p>Location : Delhi</p>

<p>Last Date : 18 Dec 2015</p>

<p>Hiring Process : Walk - In<br />IARI - Job Details</p>

<p>JRF/Traineeship/Studentship Bioinformatics job position in Indian Agricultural Research Institute (IARI) purely temporary</p>

<p>JRF</p>

<p>Qualification: i) Master’s degree in Bioinformatics or Computer Science + NET qualification, or ii) M. Tech degree in Bioinformatics or Computer Science/Engineering</p>

<p>Desirable: Efficiency to handle agricultural databases and bioinformatics tool development</p>

<p>Pay Scale :Rs 25000/- </p>

<p>Age limit : 35 years</p>

<p>Traineeship/2 Post</p>

<p>Qualification: M.Sc./M. Tech (Bioinformatics) with 60 % marks from a recognized University </p>

<p>Pay Scale :Rs. 8000/-consolidated</p>

<p>Age limit : 35 years</p>

<p>Studentship/4 Post</p>

<p>Qualification: Final year M.Sc./ M.Tech (Bioinformatics) Students from a recognized University</p>

<p>Pay Scale :Rs. 8000/-consolidated</p>

<p>Age limit : 35 years<br />How to apply</p>

<p>Walk-in-Interview will be held on 18th December 2015 at 10:00 AM at AKMU, LBS Building,IARI, Pusa Campus, New Delhi-110012. Bring self attested copies and originals of all certificates ( class 10th )onwards along with biodata in the attached format, proof of date of birth, one passport size photo, NOC from present employer, if any.</p>

<p>More at http://www.iari.res.in/index.php?option=com_jumi&amp;fileid=24&amp;Itemid=664</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37776/rhat-a-seed-and-extension-based-noisy-long-read-alignment-tool</guid>
	<pubDate>Sun, 23 Sep 2018 05:12:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37776/rhat-a-seed-and-extension-based-noisy-long-read-alignment-tool</link>
	<title><![CDATA[rHAT: a seed-and-extension-based noisy long read alignment tool]]></title>
	<description><![CDATA[<p><span>rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.</span></p><p>Address of the bookmark: <a href="https://github.com/dfguan/rHAT" rel="nofollow">https://github.com/dfguan/rHAT</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25815/jrf-bioinformatics-job-position-in-university-of-hyderabad</guid>
  <pubDate>Tue, 29 Dec 2015 01:00:18 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF Bioinformatics job position in University of Hyderabad]]></title>
  <description><![CDATA[
<p>JRF Bioinformatics</p>

<p>Eligibility : ME/M.Tech(Bio-Informatics/Bio-Chemistry Engg), MSc(Bio-Informatics)</p>

<p>Location : Hyderabad</p>

<p>Last Date : 30 Dec 2015</p>

<p>Hiring Process : Written-test<br />University of Hyderabad</p>

<p>JRF Bioinformatics job position in University of Hyderabad </p>

<p>Project Entitled : Programming protective humoral responses with novel vaccine formulations against Dengue Virus</p>

<p>Essential Qualifications : M. Sc. in Life Sciences/Bioinformatics/ or M. Tech in Bioinformatics with a minimum of 60% marks and with CSIR-UGC JRF/NET or valid GATE score are preferred. Desirable : Candidates should have six months to one year hands on experience in molecular biology techniques like gene cloning, protein expression and purification, hands on various nano-formulations for drug/vaccine delivery, immunological assays including animal handling, immunizations, T cells and B cell assays or Candidate should have strong background in Bioinformatics and computational Biology, good programming skill particularly proficiency in R/PERL/PYTHON. Candidates interested in above position should send a one page statement clearly explaining how their skills are relevant to the above said position. The candidates should also enclose detailed CV and the name/Email IDs of three references</p>

<p>Fellowship : Rs. 16,000 p.m. + 30% H.R.A. for the first two years (Revised DBT fellowship guidelines maybe applicable)</p>

<p>Duration : The appointment will be on temporary basis for a period of one year. Based on performance, the appointment could be extended till the end of project<br /> <br />How to apply</p>

<p>Submit your application (hardcopy) in a closed envelope to Dr.Nooruddin<br />Khan, Room S-66B,Department of Biotechnology and Bioinfromatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046 or E mail: nklabsls@gmail.com. Last date for receipt of applications is on or before 30.12.2015</p>

<p>More at http://uohyd.ac.in/index.php/component/content/article/87-administration/recruitments/129</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40217/shouji-a-fast-and-efficient-pre-alignment-filter-for-sequence-alignment</guid>
	<pubDate>Mon, 04 Nov 2019 07:09:45 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40217/shouji-a-fast-and-efficient-pre-alignment-filter-for-sequence-alignment</link>
	<title><![CDATA[Shouji: a fast and efficient pre-alignment filter for sequence alignment]]></title>
	<description><![CDATA[<p>The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes.</p>
<p>&nbsp;<img src="https://github.com/BilkentCompGen/Shoji/raw/master/Figure1-GitHub.png" alt="image" style="border: 0px;"></p>
<p>We introduce Shouji, a highly parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator design that adopts modern FPGA (field-programmable gate array) architectures to further boost the performance of our algorithm.</p>
<p>More at <a href="https://github.com/CMU-SAFARI/Shouji">https://github.com/CMU-SAFARI/Shouji</a></p><p>Address of the bookmark: <a href="https://github.com/CMU-SAFARI/Shouji" rel="nofollow">https://github.com/CMU-SAFARI/Shouji</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/25993/hoffman-lab</guid>
  <pubDate>Tue, 12 Jan 2016 02:47:41 -0600</pubDate>
  <link></link>
  <title><![CDATA[Hoffman Lab]]></title>
  <description><![CDATA[
<p>They develop machine learning techniques to better understand chromatin biology. These models and algorithms transform high-dimensional functional genomics data into interpretable patterns and lead to new biological insight.</p>

<p>https://www.pmgenomics.ca/hoffmanlab/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42405/caretta-%E2%80%93-a-multiple-protein-structure-alignment-and-feature-extraction-suite</guid>
	<pubDate>Fri, 18 Dec 2020 02:09:44 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42405/caretta-%E2%80%93-a-multiple-protein-structure-alignment-and-feature-extraction-suite</link>
	<title><![CDATA[Caretta – A multiple protein structure alignment and feature extraction suite]]></title>
	<description><![CDATA[<h3>Caretta &ndash;&nbsp;a multiple protein structure alignment and feature extraction suite</h3>
<p><span>Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments with a higher coverage than current state-of-the-art tools. Caretta is available as a GUI and command-line application and additionally outputs an aligned structure feature matrix for a given set of input structures, which can readily be used in downstream steps for supervised or unsupervised machine learning.&nbsp;</span></p><p>Address of the bookmark: <a href="http://www.bioinformatics.nl/caretta/" rel="nofollow">http://www.bioinformatics.nl/caretta/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33942/mulan-multiple-sequence-local-alignment-and-conservation-visualization-tool</guid>
	<pubDate>Thu, 20 Jul 2017 08:02:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33942/mulan-multiple-sequence-local-alignment-and-conservation-visualization-tool</link>
	<title><![CDATA[Mulan: MUltiple sequence Local AligNment and conservation visualization tool]]></title>
	<description><![CDATA[<p><span>Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It combines&nbsp;</span><a href="http://www.bx.psu.edu/miller_lab/" target="_new"><em>refine</em>&nbsp;and&nbsp;<em>tba</em></a><span>&nbsp;tools to align either "draft" or "finished" quality sequences. Mulan provides a dynamic graphical interface to align and visualize conservation profiles for evolutionarily distant and closely related species.</span><br><span></span></p>
<p><span>Input formats, automated data upload from the&nbsp;</span><a href="http://genome.ucsc.edu/" target="_new">UCSC Genome Browser</a><span>, gene annotation, annotation of repetitive elements, and progress report were previously described in the&nbsp;</span><a href="https://zpicture.dcode.org/zpInstructions.html" target="_zp">zPicture instructions</a><span>&nbsp;and we refer the users to these materials for more details. This introduction is mainly focused on some novel features unique to the Mulan.</span><span><br></span></p><p>Address of the bookmark: <a href="https://mulan.dcode.org/mulanInstructions.php" rel="nofollow">https://mulan.dcode.org/mulanInstructions.php</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

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