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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41405?offset=60</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43799/kast</guid>
	<pubDate>Wed, 23 Feb 2022 08:28:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43799/kast</link>
	<title><![CDATA[KAST]]></title>
	<description><![CDATA[<p><span>Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.</span></p><p>Address of the bookmark: <a href="https://github.com/martinjvickers/KAST" rel="nofollow">https://github.com/martinjvickers/KAST</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34734/smash-an-alignment-free-tool-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences</guid>
	<pubDate>Thu, 21 Dec 2017 08:26:57 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34734/smash-an-alignment-free-tool-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences</link>
	<title><![CDATA[SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences]]></title>
	<description><![CDATA[<p style="text-align: justify;"><span>SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences</span>. The detection is based on&nbsp;<span>relative compression</span>, namely using a FCM, also known as Markov model, of high context order (typically 20). The method has been approached with a tool (also called SMASH). For visualization, SMASH outputs a SVG image, with an ideogram output architecture, where the patterns are represented with several HSV values (only value varies). The following image, illustrating the information maps between human and chimpanzee for the several chromosomes, depicts an example:</p>
<p><a href="https://github.com/pratas/smash/blob/master/imgs/HC.png" target="_blank"><img src="https://github.com/pratas/smash/raw/master/imgs/HC.png" alt="ScreenShot" style="border: 0px;"></a></p>
<p>&nbsp;</p>
<h2>&nbsp;</h2><p>Address of the bookmark: <a href="https://github.com/pratas/smash" rel="nofollow">https://github.com/pratas/smash</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38385/decipher-a-software-toolset-for-deciphering-and-managing-biological-sequences-efficiently-using-the-r</guid>
	<pubDate>Sun, 09 Dec 2018 19:06:17 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38385/decipher-a-software-toolset-for-deciphering-and-managing-biological-sequences-efficiently-using-the-r</link>
	<title><![CDATA[DECIPHER; a software toolset for deciphering and managing biological sequences efficiently using the R]]></title>
	<description><![CDATA[<p><span>DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the&nbsp;</span><a href="http://www.r-project.org/">R</a><span>&nbsp;programming language. The&nbsp;</span><a href="http://www.r-project.org/">R</a><span>&nbsp;package is distributed as platform independent source code under the&nbsp;</span><a href="http://www.gnu.org/copyleft/gpl.html">GPL version 3 license</a><span>. Some functionality of the program is accessible online through web tools.</span></p>
<p><span style="font-size: medium; text-align: justify;">&nbsp;</span></p><p>Address of the bookmark: <a href="http://www2.decipher.codes/" rel="nofollow">http://www2.decipher.codes/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39867/gepard-allows-the-calculation-of-dotplots-even-for-large-sequences-like-chromosomes-or-bacterial-genomes</guid>
	<pubDate>Mon, 26 Aug 2019 11:38:30 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39867/gepard-allows-the-calculation-of-dotplots-even-for-large-sequences-like-chromosomes-or-bacterial-genomes</link>
	<title><![CDATA[Gepard: allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes]]></title>
	<description><![CDATA[<p>Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Reference: Krumsiek J, Arnold R, Rattei T. Gepard: A rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 2007; 23(8): 1026-8. PMID:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/pubmed/17309896" target="_blank">17309896</a></p>
<p><a href="http://cube.univie.ac.at/gepard">http://cube.univie.ac.at/gepard</a></p><p>Address of the bookmark: <a href="https://github.com/univieCUBE/gepard" rel="nofollow">https://github.com/univieCUBE/gepard</a></p>]]></description>
	<dc:creator>Jit</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/44896/jaeger-an-accurate-and-fast-deep-learning-tool-to-detect-bacteriophage-sequences</guid>
	<pubDate>Sun, 31 Aug 2025 06:30:16 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44896/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><span>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.</span></p><p>Address of the bookmark: <a href="https://github.com/MGXlab/Jaeger" rel="nofollow">https://github.com/MGXlab/Jaeger</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22431/genomic-scientist-at-udsc</guid>
  <pubDate>Thu, 28 May 2015 19:14:23 -0500</pubDate>
  <link></link>
  <title><![CDATA[Genomic Scientist at UDSC]]></title>
  <description><![CDATA[
<p>Centre for Genetic Manipulation of Crop Plants</p>

<p>Department of Genetics</p>

<p>University of Delhi South Campus</p>

<p>NEW DELHI – 110 021</p>

<p>WALK-IN-INTERVIEW FOR THE TEMPORARY POSITIONS OF RESEACH SCIENTIT &amp; LAB / FIELD ATTENDANT</p>

<p>1 Research Scientist (RS) – 3</p>

<p>    DBT, Ph. D.</p>

<p>    Experience on DNA Markers, plant genome mapping and bioinformatics</p>

<p>    Salary: 60,000 (Consolidated) + 5% annual increment</p>

<p>    Date and time: 25.06.2015 at 10:30 AM</p>

<p>These temporary positions have been sanctioned in a DBT funded project for the Phase II on ‘Centre of Excellence on genome mapping and molecular breeding of Brassicas.’</p>

<p>The applicants are requested to register their names on the day of interview in the First Floor, Biotech Centre, Centre for Genetic Manipulation of Crop Plants, Department of Genetics before the stipulated time for the interview. Only the registered eligible candidates will be interviewed on the day in the Committee Room.</p>

<p>Applicants are requested to bring all related documents, in original and a set of photocopy, for verification.</p>

<p>No TA/DA will be paid for attending the interview.</p>

<p>Advertisement:</p>

<p>www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&amp;cntnt01articleid=5492&amp;cntnt01returnid=83</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41678/gridss-the-genomic-rearrangement-identification-software-suite</guid>
	<pubDate>Sun, 17 May 2020 10:27:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41678/gridss-the-genomic-rearrangement-identification-software-suite</link>
	<title><![CDATA[GRIDSS: the Genomic Rearrangement IDentification Software Suite]]></title>
	<description><![CDATA[<p>GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.</p><p>Address of the bookmark: <a href="https://github.com/PapenfussLab/gridss" rel="nofollow">https://github.com/PapenfussLab/gridss</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44900/pegas-a-comprehensive-bioinformatic-solution-for-pathogenic-bacterial-genomic-analysis</guid>
	<pubDate>Mon, 01 Sep 2025 01:18:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44900/pegas-a-comprehensive-bioinformatic-solution-for-pathogenic-bacterial-genomic-analysis</link>
	<title><![CDATA[PeGAS: A Comprehensive Bioinformatic Solution for Pathogenic Bacterial Genomic Analysis]]></title>
	<description><![CDATA[<p><span>This is PeGAS, a powerful bioinformatic tool designed for the seamless quality control, assembly, and annotation of Illumina paired-end reads specific to pathogenic bacteria. This tool integrates state-of-the-art open-source software to provide a streamlined and efficient workflow, ensuring accurate insights into the genomic makeup of pathogenic microbial strains.</span></p>
<p><span><img src="https://github.com/liviurotiul/PeGAS/raw/main/Features.png" alt="image" style="border: 0px;"></span></p><p>Address of the bookmark: <a href="https://github.com/liviurotiul/PeGAS" rel="nofollow">https://github.com/liviurotiul/PeGAS</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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