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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44604?offset=20</link>
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	<item>
	<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>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/2791/ncbi-psi-blast-tutorial</guid>
	<pubDate>Fri, 23 Aug 2013 02:25:02 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/2791/ncbi-psi-blast-tutorial</link>
	<title><![CDATA[NCBI PSI-BLAST Tutorial]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/T3kHEieyylk" frameborder="0" allowfullscreen></iframe>http:--www.biotechnology.jhu.edu-
Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the
Basic Local Alignment Search tool and will protein and DNA sequences that
are related to a sequence that the user provides.]]></description>
	
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/11195/ncbi-gene-screencast</guid>
	<pubDate>Fri, 30 May 2014 06:21:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/11195/ncbi-gene-screencast</link>
	<title><![CDATA[NCBI Gene Screencast]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/WyFIf7YdM8A" frameborder="0" allowfullscreen></iframe>A short walkthrough of the NCBI Gene page]]></description>
	
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105</guid>
	<pubDate>Thu, 12 May 2016 13:49:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105</link>
	<title><![CDATA[Release Notes for Genome Workbench 2.10.5]]></title>
	<description><![CDATA[<p>New Features in latest release</p><ul>
<li>New ProSplign tool integrated with Genome Workbench (<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial13">Tutorial</a>,&nbsp;<a href="https://www.youtube.com/watch?v=V9UqKJprzAg&amp;feature=youtu.be" target="_blank">Video</a>)</li>
<li>New export function for BAM/cSRA coverage graphs (<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial14">Tutorial</a>)</li>
<li>New export function for alignments GFF3 format ((<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial15">Tutorial</a>))</li>
<li>Tree View: implemented new export mode based on selections (tutorial coming)</li>
<li>Tree View: added support for&nbsp;<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial3/#distance_based_circular_trees">distance based circular trees</a></li>
<li>Tree View: new rooting mode (Midpoint Root) results in more balanced trees (<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial3#reroot_tree">Tutorial</a>)</li>
<li>Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" &ndash; to re-root at mid-branch (<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial3#reroot_tree">Tutorial</a>)</li>
</ul>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29410/entrez-direct-e-utilities-on-the-unix-command-line</guid>
	<pubDate>Wed, 19 Oct 2016 08:06:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29410/entrez-direct-e-utilities-on-the-unix-command-line</link>
	<title><![CDATA[Entrez Direct: E-utilities on the UNIX Command Line]]></title>
	<description><![CDATA[<p>Entrez Direct (EDirect) is an advanced method for accessing the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.</p>
<p>EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.</p><p>Address of the bookmark: <a href="https://www.ncbi.nlm.nih.gov/books/NBK179288/" rel="nofollow">https://www.ncbi.nlm.nih.gov/books/NBK179288/</a></p>]]></description>
	<dc:creator>Anjana</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/35125/eugene-v-koonin-lab</guid>
  <pubDate>Tue, 09 Jan 2018 05:01:15 -0600</pubDate>
  <link></link>
  <title><![CDATA[Eugene V. Koonin Lab]]></title>
  <description><![CDATA[
<p>Interested in understanding the evolution of life. To obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in several major areas.</p>

<p>https://www.ncbi.nlm.nih.gov/research/groups/koonin/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/40596/igblast-a-popular-ncbi-package-for-classifying-and-analyzing-immunoglobulin-ig-and-t-cell-receptor-tcr-variable-domain-sequences</guid>
	<pubDate>Thu, 23 Jan 2020 11:34:37 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/40596/igblast-a-popular-ncbi-package-for-classifying-and-analyzing-immunoglobulin-ig-and-t-cell-receptor-tcr-variable-domain-sequences</link>
	<title><![CDATA[IgBLAST: a popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences]]></title>
	<description><![CDATA[<p>NCBI team released a new version of IgBLAST with four new improvements. IgBLAST is a popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences. Improvements are:<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></p><p>&nbsp;&nbsp;&nbsp; 1. Support for the new FWR4 annotation feature in the AIRR format, both in standard format and in the AIRR alignment format.<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></p><p>&nbsp;&nbsp;&nbsp; 2. The previous &ldquo;-penalty&rdquo; parameter was renamed as -V_penalty to be consistent with other IgBLAST penalty options.<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></p><p>&nbsp;&nbsp;&nbsp; 3. Restored constant internal BLAST search parameters for domain annotation (i.e., FWR/CDR) such that this process is not influenced by user parameters.<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></p><p>&nbsp;&nbsp;&nbsp; 4. Corrected FWR/CDR annotations for certain mouse VK and rat VH germline genes.<span style="font-size: 12.8px;">&nbsp;</span></p><p><span style="text-decoration: underline;"></span></p><p>IgBLAST 1.15.0 is available for&nbsp;<a href="https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST/" target="_blank">download</a>&nbsp;from the BLAST FTP area. See the the new&nbsp;<a href="https://ncbi.github.io/igblast/" target="_blank">manual</a>&nbsp;on GitHub for information about setting up and running IgBLAST.</p><p><span style="text-decoration: underline;"></span></p><p>&nbsp;If you have any questions or concerns, please contact&nbsp;<a href="mailto:blast-help@ncbi.nlm.nih.gov" target="_blank" title="Follow link">blast-help@ncbi.nlm.nih.gov</a><span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></p><p><span style="text-decoration: underline;"></span>&nbsp;</p>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/44342/ncbi-datasets%E2%80%AFpages</guid>
	<pubDate>Wed, 12 Jul 2023 06:29:31 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/44342/ncbi-datasets%E2%80%AFpages</link>
	<title><![CDATA[NCBI Datasets pages]]></title>
	<description><![CDATA[<p>Update! Assembly and Genome record pages now redirect to new NCBI Datasets pages. NCBI Datasets is a new resource that makes it easier to find and download genome data. Learn more: https://ncbiinsights.ncbi.nlm.nih.gov/2023/07/11/ncbi-datasets-genome-assembly-pages/&nbsp;<a href="https://ow.ly/GU3o50P8QH4"></a><a href="https://www.linkedin.com/feed/hashtag/?keywords=ncbicgr&amp;highlightedUpdateUrns=urn%3Ali%3Aactivity%3A7084592728260386816">#NCBICGR</a></p><p><span>Effective July 10, 2023, NCBI&rsquo;s Assembly and Genome record pages now redirect to&nbsp;</span>new<a href="https://www.ncbi.nlm.nih.gov/datasets/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=datasets-genome-assembly-redirect-20230711"> NCBI Datasets </a><span>pages. As&nbsp;</span><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2023/03/07/ncbi-datasets-genome-taxonomy-pages/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=datasets-genome-assembly-redirect-20230711">previously announced</a><span>, these updates are part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.  </span><span>&nbsp;</span></p><h5>The following pages have been updated:</h5><ul>
<li><span>The NCBI Assembly record pages now redirect to the new </span><a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_023065955.2/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=datasets-genome-assembly-redirect-20230711"><span>NCBI Datasets</span><strong><span> </span></strong><span>Genome</span></a><span> </span><span>record pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST. </span><span>&nbsp;</span></li>
<li><span>The NCBI</span><strong> </strong><span>Genome record pages now redirect to the </span><a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9644/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=datasets-genome-assembly-redirect-20230711"><span>NCBI Datasets</span><strong><span> </span></strong><span>Taxonomy</span></a><span> </span><span>record pages that provide a taxonomy-focused portal to genes, genomes, and additional NCBI resources.  </span><span>&nbsp;</span></li>
</ul><p><span>During this transition, you will have the option to return to the legacy Genome and Assembly record pages. We will remove the legacy pages in early 2024. </span><span>&nbsp;</span></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture</guid>
	<pubDate>Fri, 27 Sep 2013 04:24:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture</link>
	<title><![CDATA[Molecular Genetics Lecture]]></title>
	<description><![CDATA[<p><span>"Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and punctuated equilibrium and the influence of epigenetics on development theories."&nbsp;</span></p>
<p><span>"<span><strong>Robert Sapolsky</strong> is an American neuroendocrinologist, professor of biology, neuroscience, and neurosurgery at Stanford University, researcher and author" ----Wikipedia</span></span></p><p>Address of the bookmark: <a href="http://www.youtube.com/watch?v=_dRXA1_e30o" rel="nofollow">http://www.youtube.com/watch?v=_dRXA1_e30o</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36752/minmax-a-versatile-tool-for-calculating-and-comparing-synonymous-codon-usage-and-its-impact-on-protein-folding</guid>
	<pubDate>Thu, 24 May 2018 02:53:31 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36752/minmax-a-versatile-tool-for-calculating-and-comparing-synonymous-codon-usage-and-its-impact-on-protein-folding</link>
	<title><![CDATA[%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.]]></title>
	<description><![CDATA[%MM calculates whether a given gene sequence encodes amino acids using the most common codons possible, the least common codons possible, or (most typically) some combination of these extremes. See our PLoS ONE paper for more details on how the %MinMax algorithm works. 

%MinMax results are averaged over an 18-codon sliding window; hence the result for "codon window = 1" is the average codon usage for codons 1-18, codon window 2 = codons 2-19, etc.<p>Address of the bookmark: <a href="http://www.codons.org/" rel="nofollow">http://www.codons.org/</a></p>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
</item>

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