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	<link>https://bioinformaticsonline.com/related/43806?offset=30</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29683/method-in-comparative-genomics</guid>
	<pubDate>Wed, 09 Nov 2016 16:29:24 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29683/method-in-comparative-genomics</link>
	<title><![CDATA[Method in Comparative genomics !!]]></title>
	<description><![CDATA[<p>We present methods for the automatic determination of genome correspondence. The algorithms enabled the automatic identification of orthologs for more than 90% of genes and intergenic regions across the four species despite the large number of duplicated genes in the yeast genome. The remaining ambiguities in the gene correspondence revealed recent gene family expansions in regions of rapid genomic change.</p>
<p>We present methods for the identification of protein-coding genes based on their patterns of nucleotide conservation across related species. We observed the pressure to conserve the reading frame of functional proteins and developed a test for gene identification with high sensitivity and specificity. We used this test to revisit the genome of S. cerevisiae, reducing the overall gene count by 500 genes (10% of previously annotated genes) and refining the gene structure of hundreds of genes. We present novel methods for the systematic de novo identification of regulatory motifs. The methods do not rely on previous knowledge of gene function and in that way differ from the current literature on computational motif discovery. Based on the genome-wide conservation patterns of known motifs, we developed three conservation criteria that we used to discover novel motifs. We used an enumeration approach to select strongly conserved motif cores, which we extended and collapsed into a small number of candidate regulatory motifs. These include most previously known regulatory motifs as well as several noteworthy novel motifs. The majority of discovered motifs are enriched in functionally related genes, allowing us to infer a candidate function for novel motifs.</p>
<p>Our results demonstrate the power of comparative genomics to further our understanding of any species. Our methods are validated by the extensive experimental knowledge in yeast, and will be invaluable in the study of complex genomes like that of human.</p><p>Address of the bookmark: <a href="http://web.mit.edu/manoli/www/publications/Kellis_JCB_04.pdf" rel="nofollow">http://web.mit.edu/manoli/www/publications/Kellis_JCB_04.pdf</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/31018/j-circos</guid>
	<pubDate>Fri, 17 Feb 2017 09:06:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/31018/j-circos</link>
	<title><![CDATA[J-Circos]]></title>
	<description><![CDATA[<p>Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the GUI. J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.</p><p>Address of the bookmark: <a href="http://www.australianprostatecentre.org/research/software/jcircos" rel="nofollow">http://www.australianprostatecentre.org/research/software/jcircos</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44219/chromosome-breakpoint-a-breakup-to-remember</guid>
	<pubDate>Tue, 07 Mar 2023 13:31:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44219/chromosome-breakpoint-a-breakup-to-remember</link>
	<title><![CDATA[Chromosome breakpoint - a breakup to remember]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Chromosome breakpoint refers to the physical location where a chromosome is broken and rearranged. Chromosome breakage can occur spontaneously or be induced by environmental factors such as radiation, chemicals, or viruses. The rearrangement of genetic material resulting from a chromosome breakpoint can have important consequences, including the development of genetic diseases, chromosomal abnormalities, or cancer.</p><p>Chromosome breakpoints can occur in two ways: interstitial or terminal. Interstitial breakpoints occur within the chromosome, while terminal breakpoints occur at the end of the chromosome. Terminal breakpoints can lead to the loss of genetic material, whereas interstitial breakpoints can result in the duplication or deletion of genetic material.</p><p>Chromosome breakpoints can be detected using a variety of techniques, including cytogenetic analysis, fluorescence in situ hybridization (FISH), and molecular methods such as polymerase chain reaction (PCR) and next-generation sequencing (NGS). These techniques can also help identify the exact location of the breakpoint and the nature of the rearrangement, such as translocations, inversions, deletions, or duplications.</p><p>Translocations are one of the most common types of chromosome rearrangements caused by breakpoints. In a translocation, genetic material is exchanged between two different chromosomes, resulting in a balanced or unbalanced distribution of genetic material. Unbalanced translocations can cause genetic diseases or developmental abnormalities, while balanced translocations can be inherited without any apparent phenotypic effects.</p><p>Inversions occur when a chromosome segment is inverted, resulting in a change in the order of genetic material. Inversions can be pericentric, involving the centromere, or paracentric, not involving the centromere. Inversions can cause genetic diseases or phenotypic effects if they disrupt the function of essential genes or regulatory elements.</p><p>Deletions and duplications are caused by interstitial breakpoints that result in the loss or gain of genetic material. Deletions can cause genetic diseases or developmental abnormalities if they involve essential genes or regulatory elements. Duplications can also have phenotypic effects, depending on the location and size of the duplicated segment.</p><p>Chromosome breakpoints can also be involved in the formation of complex chromosomal rearrangements, such as ring chromosomes or dicentric chromosomes. These complex rearrangements can have important clinical implications, as they can cause genetic diseases or cancer.</p><p>In conclusion, chromosome breakpoints are important genetic events that can lead to the rearrangement of genetic material and have important clinical implications. The detection and characterization of chromosome breakpoints using cytogenetic, molecular, and genomic methods are essential for the diagnosis, prognosis, and treatment of genetic diseases and cancer. Further research is needed to understand the molecular mechanisms underlying chromosome breakage and to develop new therapies targeting these events.</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/26179/alignment-of-closely-related-whole-genomesscaffolds</guid>
	<pubDate>Fri, 29 Jan 2016 10:37:27 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26179/alignment-of-closely-related-whole-genomesscaffolds</link>
	<title><![CDATA[Alignment of closely related whole genomes/scaffolds]]></title>
	<description><![CDATA[<p>With the relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life. This increasing volume of data requires tools that can quickly compare multiple whole-genome sequences, millions of base pairs in length, to aid in the study of populations, pan-genomes, and genome evolution.This bookmaks have been created to report new tools for whole genome alignments.</p>
<p>Please report new whole genome alignment tools under comment sections.</p><p>Address of the bookmark: <a href="http://www.cs.utoronto.ca/~brudno/721.full.pdf" rel="nofollow">http://www.cs.utoronto.ca/~brudno/721.full.pdf</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/39704/the-rogers-lab</guid>
  <pubDate>Mon, 15 Jul 2019 08:07:44 -0500</pubDate>
  <link></link>
  <title><![CDATA[The Rogers Lab]]></title>
  <description><![CDATA[
<p>The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Drosophila, Mammoths, Elephants, Bivalves, and Frogs absolutely no amphibians. This multi-organism approach can help us understand when and why complex mutations are important for organism fitness.</p>

<p>More at http://evolscientist.com/</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44525/synorth-exploring-the-evolution-of-synteny-and-long-range-regulatory-interactions-in-vertebrate-genomes</guid>
	<pubDate>Mon, 06 May 2024 06:21:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44525/synorth-exploring-the-evolution-of-synteny-and-long-range-regulatory-interactions-in-vertebrate-genomes</link>
	<title><![CDATA[Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes]]></title>
	<description><![CDATA[<p><span>Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth&nbsp;</span><a href="http://synorth.genereg.net/" target="_blank">http://synorth.genereg.net/</a><span>&nbsp;is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.</span></p>
<p><span>More at&nbsp;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745767/</span></p><p>Address of the bookmark: <a href="http://synorth.genereg.net/" rel="nofollow">http://synorth.genereg.net/</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34328/dfast-a-flexible-prokaryotic-genome-annotation-pipeline-for-faster-genome-publication</guid>
	<pubDate>Tue, 14 Nov 2017 10:26:16 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34328/dfast-a-flexible-prokaryotic-genome-annotation-pipeline-for-faster-genome-publication</link>
	<title><![CDATA[DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication]]></title>
	<description><![CDATA[<p>We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.</p>
<div>Availability and Implementation</div>
<p>The software is implemented in Python 3 and runs in both Python 2.7 and 3.4&ndash; on Macintosh and Linux systems. It is freely available at&nbsp;<a href="https://github.com/nigyta/dfast_core/" target="">https://github.com/nigyta/dfast_core/</a>&nbsp;under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at&nbsp;<a href="https://dfast.nig.ac.jp/" target="">https://dfast.nig.ac.jp/</a>.</p><p>Address of the bookmark: <a href="https://dfast.nig.ac.jp/" rel="nofollow">https://dfast.nig.ac.jp/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34569/ksnp30-snp-detection-and-phylogenetic-analysis-of-genomes-without-genome-alignment-or-reference-genome</guid>
	<pubDate>Fri, 08 Dec 2017 16:48:40 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34569/ksnp30-snp-detection-and-phylogenetic-analysis-of-genomes-without-genome-alignment-or-reference-genome</link>
	<title><![CDATA[kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome]]></title>
	<description><![CDATA[<p><span>Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages 9-10) in the version 3.1 User Guide. Thanks to Tom Slezak for revsing the get_genbank_file3 script and to Tod Stuber (USDA) for testing version 3.1 even though he doesn't need the annotation feature. All users are encouraged to upgrade to version 3.1.&nbsp;<br></span></p><p>Address of the bookmark: <a href="https://sourceforge.net/projects/ksnp/files/" rel="nofollow">https://sourceforge.net/projects/ksnp/files/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36723/hapsembler-an-assembler-for-highly-polymorphic-genomes</guid>
	<pubDate>Tue, 22 May 2018 04:09:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36723/hapsembler-an-assembler-for-highly-polymorphic-genomes</link>
	<title><![CDATA[Hapsembler: An Assembler for Highly Polymorphic Genomes]]></title>
	<description><![CDATA[Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. 

http://compbio.cs.toronto.edu/hapsembler/<p>Address of the bookmark: <a href="http://compbio.cs.toronto.edu/hapsembler/" rel="nofollow">http://compbio.cs.toronto.edu/hapsembler/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32851/anges-reconstructing-ancestral-genomes-maps</guid>
	<pubDate>Thu, 18 May 2017 05:27:08 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32851/anges-reconstructing-ancestral-genomes-maps</link>
	<title><![CDATA[ANGES: reconstructing ANcestral GEnomeS maps]]></title>
	<description><![CDATA[<p>This page contains the software ANGES 1.01, that aims at reconstucting ancestral genome maps from homologous markers in extant related genomes.</p>
<h3>Download</h3>
<ul>
<li><a href="http://paleogenomics.irmacs.sfu.ca/ANGES/anges_1.01.tar.gz">Program, version 1.01</a>&nbsp;(July 10, 2012, documentation updated in August 2014)</li>
<li><a href="http://paleogenomics.irmacs.sfu.ca/ANGES/anges_1.01_examples_with_results.tar.gz">Examples with results (featured ancestors: boreoeutherian, amniote, yeasts, Burkholderia, monocots)</a>; please refer to the documentation of the distribution above.</li>
</ul><p>Address of the bookmark: <a href="http://paleogenomics.irmacs.sfu.ca/ANGES/" rel="nofollow">http://paleogenomics.irmacs.sfu.ca/ANGES/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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