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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32485?offset=850</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29576/impute2</guid>
	<pubDate>Thu, 27 Oct 2016 11:21:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29576/impute2</link>
	<title><![CDATA[IMPUTE2]]></title>
	<description><![CDATA[<p><strong>IMPUTE2</strong>&nbsp;is a computer program for phasing observed genotypes and imputing missing genotypes. Most people use just a couple of the program's basic functions, but we have also built up a collection of specialized and powerful options. If you are new to&nbsp;<strong>IMPUTE2</strong>, or indeed to phasing and imputation in general, we suggest that you start by learning the basics.</p>
<p>You should begin by downloading the program from&nbsp;<a href="https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download">here</a>. You will need to choose the link that matches your computing platform and then follow the instructions for opening the download package.</p>
<p>Once you have done this, you will be ready to try some example analyses on the test data that are provided with the download. The section on&nbsp;<a href="https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#examples">Examples</a>&nbsp;shows how to use the most common&nbsp;<strong>IMPUTE2</strong>&nbsp;functions. We suggest that you work through these examples and try to understand what the elements of each command are doing. If you don't understand something or would like to know if the program can perform a function that isn't listed, you can read our&nbsp;<a href="https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#faq">FAQ</a>&nbsp;or submit a question to our&nbsp;<a href="https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#mail_list">mail list</a>.</p>
<p>When you have learned the basic functionality of the program, you can use several features of this website to prepare your own analysis:</p>
<ul>
<li>Learn about&nbsp;<a href="https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#best_practices">best practices</a>&nbsp;for imputation.</li>
<li>Download&nbsp;<a href="https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference">reference data</a>&nbsp;that you can use to impute genotypes in your study.</li>
<li>Look through a complete list of&nbsp;<a href="https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#options">program options</a>.</li>
</ul><p>Address of the bookmark: <a href="https://mathgen.stats.ox.ac.uk/impute/impute_v2.html" rel="nofollow">https://mathgen.stats.ox.ac.uk/impute/impute_v2.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29603/statistical-for-biological-research</guid>
	<pubDate>Thu, 03 Nov 2016 04:59:48 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29603/statistical-for-biological-research</link>
	<title><![CDATA[Statistical for biological research]]></title>
	<description><![CDATA[<p>There is no disputing the importance of statistical analysis in biological research, but too often it is considered only after an experiment is completed, when it may be too late.</p>
<p>This collection highlights important statistical issues that biologists should be aware of and provides practical advice to help them improve the rigor of their work.</p>
<p><em>Nature Methods</em>' <strong><a href="http://www.nature.com/collections/qghhqm/pointsofsignificance">Points of Significance</a></strong> column on statistics explains many key statistical and experimental design concepts. <strong><a href="http://www.nature.com/collections/qghhqm/resources">Other resources</a></strong> include an online plotting tool and links to statistics guides from other publishers.</p><p>Address of the bookmark: <a href="http://www.nature.com/collections/qghhqm" rel="nofollow">http://www.nature.com/collections/qghhqm</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37965/kobas-a-web-server-for-geneprotein-functional-annotation-and-functional-gene-set-enrichment</guid>
	<pubDate>Fri, 19 Oct 2018 09:36:11 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37965/kobas-a-web-server-for-geneprotein-functional-annotation-and-functional-gene-set-enrichment</link>
	<title><![CDATA[KOBAS: a web server for gene/protein functional annotation and functional gene set enrichment]]></title>
	<description><![CDATA[<p><span>KOBAS 3.0 is a web server for gene/protein functional annotation (</span><a href="http://kobas.cbi.pku.edu.cn/annotate.php">Annotate</a><span>&nbsp;module) and functional gene set enrichment(Enrichment module). For Annotate module, it accepts gene list as input, including IDs or sequences, and generates annotations for each gene based on multiple databases about pathways, diseases, and Gene Ontology. For Enrichment module, it can accept either gene list or gene expression data as input, and generates enriched gene sets, corresponding name, p-value or a probability of enrichment and enrichment score based on results of multiple methods.</span></p><p>Address of the bookmark: <a href="http://kobas.cbi.pku.edu.cn/" rel="nofollow">http://kobas.cbi.pku.edu.cn/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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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>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38659/detail-annotation-of-genes</guid>
	<pubDate>Fri, 11 Jan 2019 05:23:33 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38659/detail-annotation-of-genes</link>
	<title><![CDATA[Detail annotation of genes !]]></title>
	<description><![CDATA[<p>gene_info recalculated daily<br>---------------------------------------------------------------------------<br> tab-delimited<br> one line per GeneID<br> Column header line is the first line in the file.<br> Note: subsets of gene_info are available in the DATA/GENE_INFO<br> directory (described later)<br>---------------------------------------------------------------------------</p>
<p>tax_id:<br> the unique identifier provided by NCBI Taxonomy<br> for the species or strain/isolate</p>
<p>GeneID:<br> the unique identifier for a gene<br> ASN1: geneid</p>
<p>Symbol:<br> the default symbol for the gene<br> ASN1: gene-&gt;locus</p>
<p>LocusTag:<br> the LocusTag value<br> ASN1: gene-&gt;locus-tag</p>
<p>Synonyms:<br> bar-delimited set of unofficial symbols for the gene</p>
<p>dbXrefs:<br> bar-delimited set of identifiers in other databases<br> for this gene. The unit of the set is database:value.<br> Note that HGNC and MGI include 'HGNC' and 'MGI', respectively,<br> in the value part of their identifier. Consequently,<br> dbXrefs for these databases will appear like:<br> HGNC:HGNC:1100<br> This would be interpreted as database='HGNC', value='HGNC:1100'<br> Example for MGI:<br> MGI:MGI:104537<br> This would be interpreted as database='MGI', value='MGI:104537'</p>
<p>chromosome:<br> the chromosome on which this gene is placed.<br> for mitochondrial genomes, the value 'MT' is used.</p>
<p>map location:<br> the map location for this gene</p>
<p>description:<br> a descriptive name for this gene</p>
<p>type of gene:<br> the type assigned to the gene according to the list of options<br> provided in https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn</p>
<p><br>Symbol from nomenclature authority:<br> when not '-', indicates that this symbol is from a<br> a nomenclature authority</p>
<p>Full name from nomenclature authority:<br> when not '-', indicates that this full name is from a<br> a nomenclature authority</p>
<p>Nomenclature status:<br> when not '-', indicates the status of the name from the <br> nomenclature authority (O for official, I for interim)</p>
<p>Other designations:<br> pipe-delimited set of some alternate descriptions that<br> have been assigned to a GeneID<br> '-' indicates none is being reported.</p>
<p>Modification date:<br> the last date a gene record was updated, in YYYYMMDD format</p>
<p>Feature type:<br> pipe-delimited set of annotated features and their classes or <br> controlled vocabularies, displayed as feature_type:feature_class <br> or feature_type:controlled_vocabulary, when appropriate; derived <br> from select feature annotations on RefSeq(s) associated with the <br> GeneID</p><p>Address of the bookmark: <a href="ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/" rel="nofollow">ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29886/research-officer-at-national-tea-research-foundation</guid>
  <pubDate>Fri, 18 Nov 2016 04:19:24 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Officer at National Tea Research Foundation]]></title>
  <description><![CDATA[
<p>National Tea Research Foundation (NTRF) a registered body, requires qualified and experienced agricultural research scientist for contractual appointment as per details below :</p>

<p>Post Research Officer, NTRF, Kolkata</p>

<p>Essential Post Graduate degree in Life Science having special paper in Bioinformatics. Post Graduate degree in Bioinformatics.</p>

<p>Desirable Ph. D. in the area of computational biology or bioinformatics.</p>

<p>Job Experience Work experience on database development, capable to work independently and efficient in bioinformatics related project.</p>

<p>Job Responsibility</p>

<p>To develop database on various aspects of tea research.</p>

<p>Screening of the In-house projects of NTRF at the preliminary level.</p>

<p>Review and evaluation of In-house projects of NTRF. Technical monitoring of the In-house projects of NTRF.</p>

<p>Reviewing the final technical report of the In-house projects of NTRF.</p>

<p>Putting-up of same proposals for taking approval and sanction of the competent authority.</p>

<p>Physical and technical verification of the In-house projects of NTRF.</p>

<p>To assist in organizing seminars / workshops / meetings etc.</p>

<p>Interested candidate may appear for walk-in Interview on 17 th November, 2016</p>

<p>More Info :</p>

<p>http://www.teaboard.gov.in/pdf/Recruitment_for_the_post_of_Research_Officer_pdf7538.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39881/apollo-a-sequence-annotation-editor</guid>
	<pubDate>Tue, 27 Aug 2019 08:08:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39881/apollo-a-sequence-annotation-editor</link>
	<title><![CDATA[Apollo: a sequence annotation editor]]></title>
	<description><![CDATA[<p><span>The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them</span></p><p>Address of the bookmark: <a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2002-3-12-research0082" rel="nofollow">https://genomebiology.biomedcentral.com/articles/10.1186/gb-2002-3-12-research0082</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30015/scripts</guid>
	<pubDate>Wed, 30 Nov 2016 10:35:15 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30015/scripts</link>
	<title><![CDATA[Scripts]]></title>
	<description><![CDATA[<p>Useful script for NGS analysis.</p><p>Address of the bookmark: <a href="http://augustus.gobics.de/binaries/scripts/" rel="nofollow">http://augustus.gobics.de/binaries/scripts/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42035/pannzer-a-fully-automated-service-for-functional-annotation-of-prokaryotic-and-eukaryotic-proteins-of-unknown-function</guid>
	<pubDate>Thu, 13 Aug 2020 09:57:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42035/pannzer-a-fully-automated-service-for-functional-annotation-of-prokaryotic-and-eukaryotic-proteins-of-unknown-function</link>
	<title><![CDATA[PANNZER: a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.]]></title>
	<description><![CDATA[<p><strong>PANNZER</strong>&nbsp;(Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.</p>
<p><strong>PANNZER</strong>&nbsp;(Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and GO classes.</p>
<p>PANNZER2 processes bacterial proteomes in minutes and eukaryotic proteomes in an hour. You can use&nbsp;<a href="http://ekhidna2.biocenter.helsinki.fi/AAI/">AAI-profiler</a>&nbsp;to summarize a proteome's species neighbors and reveal taxonomic identity or contamination.</p><p>Address of the bookmark: <a href="http://ekhidna2.biocenter.helsinki.fi/sanspanz/#" rel="nofollow">http://ekhidna2.biocenter.helsinki.fi/sanspanz/#</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30102/prism</guid>
	<pubDate>Sat, 10 Dec 2016 15:19:40 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30102/prism</link>
	<title><![CDATA[PRISM]]></title>
	<description><![CDATA[<p><span>PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events.&nbsp;</span><br><br><span>PRISM and PRISM_CTX were originally designed and written by&nbsp;</span><a href="http://www.cs.toronto.edu/~brudno">Michael Brudno</a><span>&nbsp;and Yue Jiang, The original PRISM publication can be found&nbsp;</span><a href="http://bioinformatics.oxfordjournals.org/content/early/2012/07/31/bioinformatics.bts484.abstract">here</a><span>.&nbsp;</span><br><br><span>The authors may be contacted via e-mail at:&nbsp;</span><em>prism at cs.toronto.edu</em><span>.&nbsp;</span><br><br><span>Additional information is available in the&nbsp;</span><a href="http://compbio.cs.toronto.edu/prism/PRISM_README">PRISM README</a><span>&nbsp;file and&nbsp;</span><a href="http://compbio.cs.toronto.edu/prism/PRISM_CTX_README">PRISM_CTX README</a><span>&nbsp;file.&nbsp;</span></p>
<p>http://compbio.cs.toronto.edu/prism/</p><p>Address of the bookmark: <a href="http://compbio.cs.toronto.edu/prism/" rel="nofollow">http://compbio.cs.toronto.edu/prism/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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