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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/37751?offset=50</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/41230/curated-set-of-ribosomal-rna-rrna-reference-sequences-targeted-loci-with-verifiable-organism</guid>
	<pubDate>Sun, 23 Feb 2020 02:17:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/41230/curated-set-of-ribosomal-rna-rrna-reference-sequences-targeted-loci-with-verifiable-organism</link>
	<title><![CDATA[Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism]]></title>
	<description><![CDATA[<p>MCBI have a curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal samples. To provide easy access to these sequences, we recently added a separate rRNA/ITS databases section on the nucleotide BLAST page for these targeted sequences that makes it convenient to quickly identify source organisms. The new databases are: </p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *16S ribosomal RNA (Bacteria and Archaea)</p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *18S ribosomal RNA sequences (SSU) from Fungi type and reference material&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *28S ribosomal RNA sequences (LSU) from Fungi type and reference material</p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Internal transcribed spacer region (ITS) from Fungi type and reference material</p><p>You can also download these from the BLAST db FTP area.&nbsp; See the <a href="https://go.usa.gov/xdEBX" target="_blank">NCBI Insights post</a> for more detail. </p><p>Useful links</p><p>-----------------</p><p><a href="https://go.usa.gov/xdEj5" target="_blank">BLAST form with rRNA/ITS databases</a></p><p><a href="https://ftp.ncbi.nlm.nih.gov/blast/db/" target="_blank">BLAST db download</a></p><p><a href="https://www.ncbi.nlm.nih.gov/refseq/targetedloci/" target="_blank">Targeted loci</a></p><p><span style="color: black;">If you have any questions or concerns, please contact <a href="mailto:blast-help@ncbi.nlm.nih.gov" target="_blank" title="Follow link">blast-help@ncbi.nlm.nih.gov<sup><span style="color: black; text-decoration: none;"><img src="https://mail.google.com/mail/u/0?ui=2&amp;ik=024a8aa0b9&amp;attid=0.1&amp;permmsgid=msg-f:1659255165855446848&amp;th=1706dbc8408bb740&amp;view=fimg&amp;sz=s0-l75-ft&amp;attbid=ANGjdJ_drW2ArYDNLoHrQh36gm6rp2Std8ZUSplCzP6bYQSQYBsQfZ_85vOujXOdTRdaLxrR7QeEBVUbyACPBJHhFUeIglX8G7Ew7TcclzhvO7fJhiz7sIdkkDgZ7QA&amp;disp=emb" alt="https://jira.ncbi.nlm.nih.gov/images/icons/mail_small.gif" width="13" height="12" style="border: 0px;"></span></sup></a></span></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/42296/igblast-117-is-now-available-with-improved-identification-of-productive-v-gene-sequences</guid>
	<pubDate>Sun, 01 Nov 2020 16:52:58 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/42296/igblast-117-is-now-available-with-improved-identification-of-productive-v-gene-sequences</link>
	<title><![CDATA[IgBLAST 1.17 is now available with improved identification of productive V gene sequences]]></title>
	<description><![CDATA[<p>A new release of&nbsp;<a href="https://go.usa.gov/x7WMc" target="_blank">IgBLAST</a>&nbsp;(1.17), the popular package for classifying and analyzing immunoglobulin and T cell receptor sequences, is now available on the&nbsp;<a href="https://go.usa.gov/x7WMc" target="_blank">web</a>&nbsp;and from the&nbsp;<a href="https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST" target="_blank">FTP site</a>. The updated package is better at identifying productive V gene sequences. We added a new field , &ldquo;V frame shift&rdquo;, to the IgBLAST output to indicate whether the V gene translation frame contains a frame-shift. We have also updated the definition of a productive V(D)J sequence to now exclude those with internal frame shifts.</p><p>See the&nbsp;<a href="https://ncbi.github.io/igblast/" target="_blank">new IgBLAST manual</a>&nbsp;on the NCBI GitHub site for more information on setting up and running IgBLAST.</p><p>If you have any questions or concerns, please email us at&nbsp;<a href="mailto:blast-help@ncbi.nlm.nih.gov" target="_blank">blast-help@ncbi.nlm.nih.gov</a></p><p>&nbsp;</p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44234/steps-to-find-palindrome-in-genomes</guid>
	<pubDate>Thu, 09 Mar 2023 02:56:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44234/steps-to-find-palindrome-in-genomes</link>
	<title><![CDATA[Steps to find palindrome in genomes !]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Palindromes are sequences of nucleotides that read the same backward as forward. They can be present in genomes and have various biological functions. Here are some methods for discovering palindromes in genomes:</p><ol>
<li>
<p>Direct sequence search: One of the simplest ways to discover palindromes is to search the genome sequence directly for palindromic sequences using pattern matching tools, such as regular expressions or string algorithms. This approach can be useful for discovering simple palindromes, but may miss more complex palindromic structures.</p>
</li>
<li>
<p>Dot plot analysis: Dot plot analysis is a graphical method that can be used to identify palindromic regions in a genome. It involves plotting the genome sequence against itself and examining the diagonal patterns that emerge. Palindromic regions will appear as symmetrical patterns along the diagonal.</p>
</li>
<li>
<p>Restriction enzyme analysis: Some restriction enzymes, such as EcoRI and HindIII, recognize palindromic sequences and cleave DNA at these sites. By digesting the genome with these enzymes and examining the resulting fragments, palindromic regions can be identified.</p>
</li>
<li>
<p>Next-generation sequencing: High-throughput sequencing technologies, such as PacBio and Oxford Nanopore, can generate long reads that can span entire palindromic regions. By mapping these reads to the genome, palindromic regions can be identified and characterized.</p>
</li>
<li>
<p>Comparative genomics: Comparing the genomes of related species can also reveal palindromic regions that are conserved across evolutionarily divergent lineages. This approach can help identify functional palindromes that are under selective pressure.</p>
</li>
</ol><p>Overall, the discovery of palindromic sequences in genomes can be accomplished using a variety of methods, each with their own advantages and limitations. A combination of these methods can provide a comprehensive understanding of the palindromic landscape of a genome.</p></div></div></div></div></div></div></div></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44878/jaeger-an-accurate-and-fast-deep-learning-tool-to-detect-bacteriophage-sequences</guid>
	<pubDate>Thu, 14 Aug 2025 04:02:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44878/jaeger-an-accurate-and-fast-deep-learning-tool-to-detect-bacteriophage-sequences</link>
	<title><![CDATA[Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences]]></title>
	<description><![CDATA[<p dir="auto">Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.</p>
<p dir="auto">The performance of the Jaeger workflow can be significantly increased by utilizing GPUs. To enable GPU support, the CUDA Toolkit and cuDNN library must be accessible to conda.</p>
<div>
<pre><code># setup bioconda
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

# create conda environment and install jaeger
mamba create -n jaeger -c nvidia -c conda-forge cuda-nvcc "python&gt;=3.9,&lt;3.12" pip jaeger-bio


# activate environment
conda activate jaeger</code></pre>
</div><p>Address of the bookmark: <a href="https://github.com/MGXlab/Jaeger" rel="nofollow">https://github.com/MGXlab/Jaeger</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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