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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/22807?offset=960</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29635/r-graphs</guid>
	<pubDate>Fri, 04 Nov 2016 10:48:00 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29635/r-graphs</link>
	<title><![CDATA[R Graphs !!]]></title>
	<description><![CDATA[<p><span>The blog is a collection of script examples with example data and output plots. R produce excellent quality graphs for data analysis, science and business presentation, publications and other purposes. Self-help codes and examples are provided. Enjoy nice graphs !!</span></p><p>Address of the bookmark: <a href="http://rgraphgallery.blogspot.be/" rel="nofollow">http://rgraphgallery.blogspot.be/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/29652/bioistats-ppt</guid>
	<pubDate>Tue, 08 Nov 2016 07:09:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/file/view/29652/bioistats-ppt</link>
	<title><![CDATA[Bioistats PPT]]></title>
	<description><![CDATA[<p>Basics concepts of&nbsp;Probability: The Study of Randomness</p><p>Biostatistics is the application of statistics to a wide range of topics in biology. The science of biostatistics encompasses the design of biological experiments, especially in medicine, pharmacy, agriculture and fishery; the collection, summarization, and analysis of data from those experiments; and the interpretation of, and inference from, the results. A major branch of this is medical biostatistics, which is exclusively concerned with medicine and health.</p>]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/29652" length="1663809" type="application/pdf" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29679/comparative-genomics-educational-material-and-papers-bookmarks</guid>
	<pubDate>Wed, 09 Nov 2016 16:23:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29679/comparative-genomics-educational-material-and-papers-bookmarks</link>
	<title><![CDATA[Comparative genomics educational material and papers bookmarks]]></title>
	<description><![CDATA[<p><span>Alignment of the porcine genome against seven other mammalian genomes (</span><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#supplementary-information">Supplementary Information</a><span>) identified homologous synteny blocks (HSBs). Using porcine HSBs and stringent filtering criteria, 192 pig-specific evolutionary breakpoint regions (EBRs) were located. The number of porcine EBRs </span><span>is comparable to the number of bovine-lineage-specific EBRs (100) reported earlier using a slightly lower resolution (500</span><span><span>&thinsp;</span></span><span>kilobases (kb)), indicating that both lineages evolved with an average rate of ~2.1 large-scale rearrangements per million years after the divergence from a common cetartiodactyl ancestor ~60</span><span><span>&thinsp;</span></span><span>Myr ago</span><sup><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#ref2" title="Meredith, R. W. et al. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334, 521-524 (2011)">2</a></sup><span>. This rate compares to ~1.9 rearrangements per million years within the primate lineage (</span><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#supplementary-information">Supplementary Table 11</a><span>). A total of 20 and 18 cetartiodactyl EBRs (shared by pigs and cattle) were detected using the pig and human genomes as a reference, respectively.</span></p><p>Address of the bookmark: <a href="http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html" rel="nofollow">http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29849/ra-bioinformatics-at-national-institute-of-cancer-prevention-research-icmr</guid>
  <pubDate>Thu, 17 Nov 2016 04:11:09 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at NATIONAL INSTITUTE OF CANCER PREVENTION &amp; RESEARCH (ICMR)]]></title>
  <description><![CDATA[
<p>NATIONAL INSTITUTE OF CANCER PREVENTION &amp; RESEARCH (ICMR)</p>

<p>Noida 201301 (U.P)</p>

<p>Applications are invited upto 21.11.2016 from interested candidates as per details available on NICPR website (www.nicpr.res.in)/ ICMR website (www.icmr.nic.in) to fill up following temporary position in the time bound DHR Project entitled “Next generation EGFR inhibitor identification using ligand based QSAR technique” under Dr. Subhash M. Agarwal, Scientist-D, Division of Bioinformatics.</p>

<p>Research Assistant (One)</p>

<p>Rs.27000/- p.m. (Fixed/temporary)</p>

<p>Essential: M.Sc. in Bioinformatics or related field.</p>

<p>Desirable: Experience in QSAR and structure based drug designing.</p>

<p>More Info : www.icmr.nic.in/icmrnews/NICPR_Advertisement%20for%20RA.pdf</p>
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  <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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30018/bipype</guid>
	<pubDate>Thu, 01 Dec 2016 08:47:38 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30018/bipype</link>
	<title><![CDATA[bipype]]></title>
	<description><![CDATA[<p><span>Bipype is a very useful program, which prepare a lot of types of bioinformatics analyses. There are three input options: amplicons, WGS (whole genome sequences) and metatranscriptomic data. If amplicons are input data, then bipype does reconstruction and pairs merging. After that biodiversity is searching. There are two types of searching depending on the amplicons types (ITS or 16S). If WGS are chosen, then bipype finds the SA coordinates of the input reads and generates alignments in the SAM format given single-end reads, aligns reads to reference sequence(s). All of these analyses will be shown with Krona program, which allows to show hierarchical data with pie charts.</span></p><p>Address of the bookmark: <a href="https://readthedocs.org/projects/bipype/" rel="nofollow">https://readthedocs.org/projects/bipype/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30355/meme-suite</guid>
	<pubDate>Fri, 23 Dec 2016 08:49:55 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30355/meme-suite</link>
	<title><![CDATA[MEME suite]]></title>
	<description><![CDATA[<p>Motif based sequence analysis suits&nbsp;</p>
<p>The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.</p>
<p>The MEME Suite supports motif-based analysis of DNA, RNA and protein sequences. It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (MEME), which have complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2). In addition to motif discovery, the MEME Suite provides tools for scanning sequences for matches to motifs (FIMO, MAST and GLAM2Scan), scanning for clusters of motifs (MCAST), comparing motifs to known motifs (Tomtom), finding preferred spacings between motifs (SpaMo), predicting the biological roles of motifs (GOMo), measuring the positional enrichment of sequences for known motifs (CentriMo), and analyzing ChIP-seq and other large datasets (MEME-ChIP).</p>
<p>The MEME Suite is comprised of a collection of tools that work together, as shown below. Not all the tools are available as webservices, so to get the full power of the MEME Suite you will need to&nbsp;<a href="http://meme-suite.org/doc/download.html">download</a>&nbsp;and&nbsp;<a href="http://meme-suite.org/doc/install.html">install</a>&nbsp;a local copy of the software. To see what has changed recently you can peruse the&nbsp;<a href="http://meme-suite.org/doc/release-notes.html">release notes</a>.</p>
<p>http://meme-suite.org/</p><p>Address of the bookmark: <a href="http://meme-suite.org/" rel="nofollow">http://meme-suite.org/</a></p>]]></description>
	<dc:creator>Bulbul</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30459/prodigal-prokaryotic-dynamic-programming-genefinding-algorithm</guid>
	<pubDate>Thu, 29 Dec 2016 03:26:45 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30459/prodigal-prokaryotic-dynamic-programming-genefinding-algorithm</link>
	<title><![CDATA[Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)]]></title>
	<description><![CDATA[<p><span>Prodigal (</span><strong>Pro</strong><span>karyotic&nbsp;</span><strong>Dy</strong><span>namic Programming&nbsp;</span><strong>G</strong><span>enefinding&nbsp;</span><strong>Al</strong><span>gorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include:</span></p>
<ul>
<li><strong>Speed</strong>: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.</li>
<li><strong>Accuracy</strong>: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly).</li>
<li><strong>Specificity</strong>: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%.</li>
<li><strong>GC-Content Indifferent</strong>: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the&nbsp;<em>Pseudomonas aeruginosa</em>&nbsp;curated annotations.</li>
<li><strong>Metagenomic Version</strong>: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.</li>
<li><strong>Ease of Use</strong>: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.</li>
<li><strong>Open Source</strong>: Prodigal source code is freely available under the General Public License.</li>
</ul>
<p>&nbsp;</p>
<div style="text-align: center;"><strong>Download the latest version of Prodigal at&nbsp;<a href="http://github.com/hyattpd/prodigal/releases/">the Prodigal github page.</a></strong>&nbsp;<br>or&nbsp;<br><strong>Browse the&nbsp;<a href="http://github.com/hyattpd/prodigal/wiki">wiki documenation.</a></strong>&nbsp;</div><p>Address of the bookmark: <a href="http://prodigal.ornl.gov/" rel="nofollow">http://prodigal.ornl.gov/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30555/yaha</guid>
	<pubDate>Fri, 20 Jan 2017 05:38:05 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30555/yaha</link>
	<title><![CDATA[YAHA]]></title>
	<description><![CDATA[<p>YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints.</p>
<p><strong>Availability:</strong> YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from <a href="http://faculty.virginia.edu/irahall/YAHA" target="pmc_ext">http://faculty.virginia.edu/irahall/YAHA</a>.</p>
<p><strong>Contact:</strong></p>
<p>http://genome.wustl.edu/people/groups/detail/hall-lab/</p><p>Address of the bookmark: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463118/" rel="nofollow">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463118/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/30657/studentship</guid>
  <pubDate>Tue, 24 Jan 2017 04:26:14 -0600</pubDate>
  <link></link>
  <title><![CDATA[Studentship]]></title>
  <description><![CDATA[
<p>Advt. No. ACBR/BTBI/BIF/Manpower/ADV/16-17<br />Research Associate/ Studentship/ Traineeship Jobs opportunity in  University of Delhi - Dr. B.R. Ambedkar Center for Biomedical Research (ACBR) on temporary basis<br />Studentship<br />No. of Post : 01<br />Qualifications : Applicants who are pursuing Post Graduate Degree course/ Diploma in Bioinformatics/ Biomedical Sciences/ Biotechnology/Life Sciences/Chemistry/ Biochemistry with a programme in Bioinformatics to carry out the project.<br />Remuneration : Rs. 8,000/-<br />Traineeship<br />No. of Post : 01<br />Qualifications : Applicants who have completed their Post Graduate degree in Bioinformatics /Biomedical Sciences/Biotechnology/Life Sciences/Chemistry/Biochemistry or any other branch of Life Sciences with knowledge in Bioinformatics<br />Remuneration : Rs. 8,000/-<br />Research Associate<br />No. of Post : 01<br />Qualifications : Ph.D. in Bio-Medical Sciences/Bioinformatics/ Biotechnology/Life Sciences/ Chemistry/ Bio-Chemistry and related areas<br />Remuneration : Rs. 36,000/-</p>

<p>Applicant are required to bring applications on plain paper, stating the name, address, date of birth. educational qualifications and experiences and Institute, along with attested photocopies of mark sheets and certificates etc. at the time of Interview. Applications should also be sent by Entail to Dr. Madhu Chopra, Coordinator, BIF Facility. Email: acbrdu.blisnet@nic.in;  mchopradu@gmail.com.<br />Interview Date : 13.02.2017<br />Time : 10:00 am-12:00 noon<br />Venue : ACBR</p>
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