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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/39624?offset=150</link>
	<atom:link href="https://bioinformaticsonline.com/related/39624?offset=150" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37759/pandaseq-is-a-program-to-align-illumina-reads-optionally-with-pcr-primers-embedded-in-the-sequence-and-reconstruct-an-overlapping-sequence</guid>
	<pubDate>Fri, 21 Sep 2018 10:19:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37759/pandaseq-is-a-program-to-align-illumina-reads-optionally-with-pcr-primers-embedded-in-the-sequence-and-reconstruct-an-overlapping-sequence</link>
	<title><![CDATA[PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.]]></title>
	<description><![CDATA[<p>Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via:</p>
<pre><code>sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config
</code></pre>
<p>On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must be installed, then:</p>
<pre><code>sudo fink install bzip2-dev pkgconfig</code></pre><p>Address of the bookmark: <a href="https://github.com/neufeld/pandaseq" rel="nofollow">https://github.com/neufeld/pandaseq</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/44364/genbank-release-2570-is-now-available</guid>
	<pubDate>Wed, 23 Aug 2023 00:23:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/44364/genbank-release-2570-is-now-available</link>
	<title><![CDATA[GenBank release 257.0 is now available!]]></title>
	<description><![CDATA[<p><span>GenBank release 257.0 is now available! This release has 25.10 trillion bases and 3.69 billion records. Learn more:&nbsp;https://ncbiinsights.ncbi.nlm.nih.gov/2023/08/21/genbank-release-257/</span><a href="https://ow.ly/zHbV50PBE5o"><br /></a></p><p><a href="https://www.ncbi.nlm.nih.gov/genbank/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=genbank-release-20230821">GenBank</a>&nbsp;release 257.0 (8/15/2023) is now available on the&nbsp;<a href="https://ftp.ncbi.nlm.nih.gov/genbank/">NCBI FTP site</a>. This release has 25.10 trillion bases and 3.69 billion records.</p><p><strong>The current release has:</strong></p><ul>
<li>246,119,175 traditional records containing 2,112,058,517,945 base pairs of sequence data</li>
<li>2,631,493,489 WGS records containing 22,294,446,104,543 base pairs of sequence data</li>
<li>686,271,945 bulk-oriented TSA records containing 646,176,166,908 base pairs of sequence data</li>
<li>124,421,006 bulk-oriented TLS records containing 48,289,699,026 base pairs of sequence data</li>
</ul>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36758/pbalign-maps-pacbio-reads-to-reference-sequences-and-saves-alignments-to-a-bam-file</guid>
	<pubDate>Thu, 24 May 2018 10:06:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36758/pbalign-maps-pacbio-reads-to-reference-sequences-and-saves-alignments-to-a-bam-file</link>
	<title><![CDATA[pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file]]></title>
	<description><![CDATA[pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver option is specified.<p>Address of the bookmark: <a href="https://github.com/PacificBiosciences/pbalign" rel="nofollow">https://github.com/PacificBiosciences/pbalign</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37987/ropebwt2-incremental-construction-of-fm-index-for-dna-sequences</guid>
	<pubDate>Thu, 25 Oct 2018 04:48:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37987/ropebwt2-incremental-construction-of-fm-index-for-dna-sequences</link>
	<title><![CDATA[RopeBWT2: Incremental construction of FM-index for DNA sequences]]></title>
	<description><![CDATA[<p><span>RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of&nbsp;</span><a href="http://dx.doi.org/10.1007/978-3-642-21458-5_20">BCR</a><span>&nbsp;and&nbsp;</span><a href="http://dfmi.sourceforge.net/">dynamic FM-index</a><span>. Nonetheless, ropeBWT2 is unique in that it may&nbsp;</span><em>implicitly</em><span>sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index.</span></p><p>Address of the bookmark: <a href="https://github.com/lh3/ropebwt2" rel="nofollow">https://github.com/lh3/ropebwt2</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38501/fgenesh-program-for-predicting-multiple-genes-in-genomic-dna-sequences</guid>
	<pubDate>Thu, 20 Dec 2018 11:55:08 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38501/fgenesh-program-for-predicting-multiple-genes-in-genomic-dna-sequences</link>
	<title><![CDATA[FGENESH - Program for predicting multiple genes in genomic DNA sequences]]></title>
	<description><![CDATA[<p>FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu&nbsp;<em>et al</em>. (2002) Science 296:79) and was used to produce 87% of all high-evidence predicted genes (Goff&nbsp;<em>et al</em>. (2002) Science 296:79).</p><p>Address of the bookmark: <a href="http://www.softberry.com/berry.phtml?topic=fgenesh&amp;group=help&amp;subgroup=gfind" rel="nofollow">http://www.softberry.com/berry.phtml?topic=fgenesh&amp;group=help&amp;subgroup=gfind</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40212/kalign-fast-multiple-sequence-alignment-program-for-biological-sequences</guid>
	<pubDate>Fri, 01 Nov 2019 00:20:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40212/kalign-fast-multiple-sequence-alignment-program-for-biological-sequences</link>
	<title><![CDATA[Kalign: fast multiple sequence alignment program for biological sequences.]]></title>
	<description><![CDATA[<p><span>Kalign is a fast multiple sequence alignment program for biological sequences.</span></p>
<p>Align sequences and output the alignment in MSF format:</p>
<pre><code>kalign -i BB11001.tfa -f msf  -o out.msf
</code></pre>
<p>Align sequences and output the alignment in clustal format:</p>
<pre><code>kalign -i BB11001.tfa -f clu -o out.clu
</code></pre>
<p>Re-align sequences in an existing alignment:</p>
<pre><code>kalign -i BB11001.msf  -o out.afa
</code></pre>
<p>Reformat existing alignment:</p>
<pre><code>kalign -i BB11001.msf -r afa -o out.afa</code></pre><p>Address of the bookmark: <a href="https://github.com/TimoLassmann/kalign" rel="nofollow">https://github.com/TimoLassmann/kalign</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<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>
</item>
<item>
	<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>
</item>
<item>
	<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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26252/recombination-detection-tool</guid>
	<pubDate>Tue, 02 Feb 2016 10:11:14 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26252/recombination-detection-tool</link>
	<title><![CDATA[Recombination detection tool]]></title>
	<description><![CDATA[<p>A program to detect recombination hotspots using population genetic data.</p>
<p>More at https://github.com/auton1/LDhot</p><p>Address of the bookmark: <a href="https://github.com/auton1/LDhot" rel="nofollow">https://github.com/auton1/LDhot</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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