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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30018?offset=710</link>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29998/csir-nehru-science-postdoctoral-research-fellowship</guid>
  <pubDate>Tue, 29 Nov 2016 12:34:59 -0600</pubDate>
  <link></link>
  <title><![CDATA[CSIR Nehru Science Postdoctoral Research Fellowship]]></title>
  <description><![CDATA[
<p>CSIR Nehru Science Postdoctoral Research Fellowship</p>

<p>About Fellowship: <br />CSIR Nehru Science Postdoctoral Research Fellowship Scheme is an Research Fellowship awarded/given by HRD Ministry, Govt. of India every year to more than 100 fellows.</p>

<p>It was started to identify promising and young researchers with novel ideas and provide them research opportunities in the areas of basic science, engineering, medicine &amp; agriculture.</p>

<p>The fellowship aims at facilitating their transition from mentored to independent research career.</p>

<p>In addition, check these ICTS Research Fellowships:<br />1.) Max-Planck Partner Group Fellowships 2017-18<br />2.) ICTS-Simons Postdoctoral Fellowships 2017<br />3.) ICTS Post Doctoral Fellowships 2017<br />4.) Airbus Prize Postdoctoral Fellowship 2017-18</p>

<p>Eligibility: To be eligible for this fellowship, you:<br />1.) PhD degree (within 3 years of award of PhD degree), OR<br />2.) Those who have submitted PhD theses.<br />3.) Applicants should have research publications in good impact factor SCI journals.<br />4.) Indian nationals, Persons of Indian Origin (PIO) &amp; Overseas Citizen of India (OCI), a can also apply.<br />5.) Maximum Age Limit: 32 years.</p>

<p>Duration: <br />– 2 Years.<br />– extendable for a maximum of 1 more year based on performance.</p>

<p>Remuneration: <br />– Rs. 50,000/- per month plus House Rent Allowance (HRA)<br />– A contingency grant of Rs. 3.0 lakh per annum.<br />– 25% of the contingency grant can be used for domestic and international travel.</p>

<p>Mode of Selection: You can apply throughout the year, but selection will be made twice a year, in June and December.</p>

<p>How to Apply: <br />– Read the instructions, given at Annexure-I in this PDF file.<br />– And, application form is given as, Annexure-II.<br />– Fill the form &amp; send it to the given address in the PDF file.</p>

<p>Deadline: Rolling Deadline (Applications accepted throughout the year)</p>

<p>Also See: Research Internship/ Fellowship in India:<br />1.) IIT Bombay Research Internship Awards Programme 2016-17<br />2.) IIT Delhi Internship Program 2016-17<br />3.) DAAD WISE – International Internship in Germany<br />4.) Summer Research Fellowship Programme| JNCASR Bangalore<br />5.) Indian Academy of Sciences Summer Internships 2017<br />6.) Winter Internship – IIT Bombay NPDE-TCA<br />7.) Viterbi – India Program 2017 | Research Internship in US<br />8.) Internship – Centre for Stem Cell Research, Vellore</p>

<p>Accommodation &amp; other benefits: <br />– Accommodation may be provided by CSIR, if available.<br />– Medical benefits as per CSIR norms.</p>

<p>For more details: <br />– Check this PDF Notification of Fellowship.<br />– List of CSIR Labs &amp; their work/activities can be seen at www.csir.res.in.</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/30198/faculty-at-indian-institute-of-science-education-and-research-berhampur</guid>
  <pubDate>Mon, 19 Dec 2016 03:34:26 -0600</pubDate>
  <link></link>
  <title><![CDATA[Faculty at Indian Institute of Science Education and Research Berhampur]]></title>
  <description><![CDATA[
<p>Advt. No: IISERBPR/DoFA/2016/2</p>

<p>Advertisement for Faculty Positions</p>

<p>The IISER Berhampur, an Institute of national importance, established through an act of Parliament is an autonomous organization under the Ministry of HRD, Govt. of India, to promote quality education and cutting edge research in basic sciences and to provide a platform for the faculty to engage in high quality education, at undergraduate and postgraduate levels. The Institute invites applications for faculty positions at the level of Assistant Professor (C) /Assistant Professor in the following disciplines:</p>

<p>1. Biological Sciences</p>

<p>2. Chemistry</p>

<p>3. Computer Sciences</p>

<p>4. Mathematics</p>

<p>5. Physics</p>

<p>Only hard copy of application in the prescribed format, via Speed Post should be sent to the Dean, Faculty Affairs, IISER Berhampur, Industrial Training Institute (ITI) Berhampur, Engineering School Road, Berhampur - 760 010, Ganjam District, Odisha, before 1700 hrs., December 30, 2016.</p>

<p>http://www.iiserbpr.ac.in</p>

<p>More Info : http://www.iiserbpr.ac.in/vacancies/Advertisement%20for%20Faculty%20Positions%20at%20IISER%20Berhampur.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30076/sga-string-graph-assembler</guid>
	<pubDate>Thu, 08 Dec 2016 05:08:59 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30076/sga-string-graph-assembler</link>
	<title><![CDATA[SGA: String Graph Assembler]]></title>
	<description><![CDATA[<p><span>SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.</span></p>
<p><span>More at</span></p>
<p><span>https://github.com/jts/sga</span></p>
<p>SGA dependencies:<br> -google sparse hash library (http://code.google.com/p/google-sparsehash/)<br> -the bamtools library (https://github.com/pezmaster31/bamtools)<br> -zlib (http://www.zlib.net/)<br> -(optional but suggested) the jemalloc memory allocator (http://www.canonware.com/jemalloc/download.html)</p><p>Address of the bookmark: <a href="https://github.com/jts/sga" rel="nofollow">https://github.com/jts/sga</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30093/velvet-tutorial</guid>
	<pubDate>Fri, 09 Dec 2016 04:19:07 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30093/velvet-tutorial</link>
	<title><![CDATA[Velvet tutorial]]></title>
	<description><![CDATA[<p><span>The objective of this activity is to help you understand how to run&nbsp;</span><a href="http://evomics.org/resources/software/genomics-software/assembly/velvet/" title="Velvet">Velvet</a><span>&nbsp;in general, how to accurately estimate the insert size of a paired-end library through the use of&nbsp;</span><a href="http://evomics.org/resources/software/genomics-software/assembly/bowtie/" title="Bowtie">Bowtie</a><span>, the primary parameters of velvet, and the process involved in producing a&nbsp;</span><em>de novo</em><span>&nbsp;assembly from Illumina reads.</span></p>
<p>http://evomics.org/learning/assembly-and-alignment/velvet/</p><p>Address of the bookmark: <a href="http://evomics.org/learning/assembly-and-alignment/velvet/" rel="nofollow">http://evomics.org/learning/assembly-and-alignment/velvet/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30124/understanding-greedy-algorithms</guid>
	<pubDate>Mon, 12 Dec 2016 04:37:40 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30124/understanding-greedy-algorithms</link>
	<title><![CDATA[Understanding Greedy Algorithms]]></title>
	<description><![CDATA[<p>Learning greedy algo for biologist.&nbsp;</p>
<p>https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/</p>
<p>This webpage is also useful for the same:</p>
<p>http://learninglover.com/examples.php?id=59</p>
<p>http://www.cs.rpi.edu/~magdon/ps/conference/super_biokdd.pdf</p>
<p>https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf</p>
<p>http://schatzlab.cshl.edu/teaching/AssemblyClass/01.%20Assembly%20Intro.pdf</p>
<p>http://lsl.sinica.edu.tw/Services/Class/files/20150612449.pdf</p>
<p>http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_scs.pdf</p>
<p>https://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-43.pdf</p><p>Address of the bookmark: <a href="https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/" rel="nofollow">https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30149/mypro-a-seamless-pipeline-for-automated-prokaryotic-genome-assembly-and-annotation</guid>
	<pubDate>Thu, 15 Dec 2016 05:47:35 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30149/mypro-a-seamless-pipeline-for-automated-prokaryotic-genome-assembly-and-annotation</link>
	<title><![CDATA[MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation]]></title>
	<description><![CDATA[<p>MyPro is an improved genomics software pipeline for prokaryotic genomes. MyPro is user-friendly and requires minimal programming skills. High-quality prokaryotic genome assembly and annotation can be obtained with ease. It performed better than de novo assemblers and contig integration software. Produces more contiguous assemblies, higher N50 values and lower number of contigs.</p>
<p>More at https://sourceforge.net/projects/sb2nhri/files/MyPro/</p><p>Address of the bookmark: <a href="http://www.sciencedirect.com/science/article/pii/S0167701215001207" rel="nofollow">http://www.sciencedirect.com/science/article/pii/S0167701215001207</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30207/gam-ngs-genomic-assemblies-merger-for-next-generation-sequencing</guid>
	<pubDate>Mon, 19 Dec 2016 06:07:05 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30207/gam-ngs-genomic-assemblies-merger-for-next-generation-sequencing</link>
	<title><![CDATA[GAM-NGS: genomic assemblies merger for next generation sequencing]]></title>
	<description><![CDATA[<p><span>GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic&nbsp;</span><em>locus</em><span>&nbsp;(called&nbsp;</span><em>blocks</em><span>) are identified through reads' alignments and stored in a&nbsp;</span><em>weighted</em><span>graph. The merging phase is carried out with the help of this weighted graph that allows an&nbsp;</span><em>optimal</em><span>&nbsp;resolution of&nbsp;</span><em>local</em><span>&nbsp;problematic regions.</span></p><p>Address of the bookmark: <a href="https://github.com/vice87/gam-ngs" rel="nofollow">https://github.com/vice87/gam-ngs</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30234/last</guid>
	<pubDate>Mon, 19 Dec 2016 14:07:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30234/last</link>
	<title><![CDATA[LAST]]></title>
	<description><![CDATA[<p>LAST can:</p>
<ul>
<li>Handle&nbsp;<strong>big</strong>&nbsp;sequence data, e.g:
<ul>
<li>Compare two vertebrate genomes</li>
<li>Align billions of DNA reads to a genome</li>
</ul>
</li>
<li>Indicate the&nbsp;<a href="http://lastweb.cbrc.jp/about.html">reliability</a>&nbsp;of each aligned column.</li>
<li>Use sequence quality data&nbsp;<a href="http://nar.oxfordjournals.org/content/38/7/e100.abstract">properly</a>.</li>
<li>Compare DNA to proteins, with frameshifts.</li>
<li>Compare PSSMs to sequences</li>
<li>Calculate the likelihood of chance similarities between random sequences.</li>
<li>Do split and spliced alignment.</li>
<li><a href="http://last.cbrc.jp/doc/last-train.html">Train</a>&nbsp;alignment parameters for unusual kinds of sequence (e.g. nanopore).</li>
</ul><p>Address of the bookmark: <a href="http://last.cbrc.jp/" rel="nofollow">http://last.cbrc.jp/</a></p>]]></description>
	<dc:creator>Bulbul</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30249/genome-assembly-tutorial</guid>
	<pubDate>Tue, 20 Dec 2016 07:56:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30249/genome-assembly-tutorial</link>
	<title><![CDATA[Genome Assembly Tutorial]]></title>
	<description><![CDATA[<p><span>If genomes were completely random sequences in a statistical sense, 'overlap-consensus-layout' method would have been enough to assemble large genomes from Sanger reads. In contrast, real genomes often have long repetitive regions, and they are hard to assemble using overlap-consensus-layout approach. De Bruijn graph-based assembly approach was originally proposed to handle the assembly of repetitive regions better.</span></p>
<p><span>More at&nbsp;http://www.homolog.us/Tutorials/index.php?p=1.4&amp;s=1</span></p><p>Address of the bookmark: <a href="http://www.homolog.us/Tutorials/index.php?p=1.4&amp;s=1" rel="nofollow">http://www.homolog.us/Tutorials/index.php?p=1.4&amp;s=1</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30336/finding-patterns-in-biological-sequences</guid>
	<pubDate>Thu, 22 Dec 2016 10:30:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30336/finding-patterns-in-biological-sequences</link>
	<title><![CDATA[Finding Patterns in Biological Sequences]]></title>
	<description><![CDATA[<p>In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological verification of such patterns. Finally we list publicly available tools and databases for pattern discovery. On-line supplement is available through http://genetics.uwaterloo.ca/&sim;tvinar/cs798g/motif.</p><p>Address of the bookmark: <a href="http://engr.case.edu/li_jing/papers/00798gpattern.pdf" rel="nofollow">http://engr.case.edu/li_jing/papers/00798gpattern.pdf</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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