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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41485?offset=40</link>
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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>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42712/scientist-c-non-medical-it-expert-computer-professionalgenomicsbioinformatic-at-nimr</guid>
  <pubDate>Mon, 01 Feb 2021 13:54:06 -0600</pubDate>
  <link></link>
  <title><![CDATA[Scientist C - Non-Medical (IT Expert- Computer Professional/Genomics/Bioinformatic) at NIMR]]></title>
  <description><![CDATA[
<p>Applications are invited upto 12th February 2021 in the prescribed format (available on the websites of ICMR-NIMR) through link http://onlineapply.nimr.org.in/ up to 05:00 PM on 12th February 2021 for the following post on contract basis at NIMR, Sector-8, Dwarka, New Delhi.</p>

<p>Scientist C - Non-Medical (IT Expert- Computer Professional/Genomics/Bioinformatic)No. of posts: 01 (UR)</p>

<p>Salary (Fixed): Rs.51,000/- + HRA</p>

<p>Essential Qualification: Candidate should possess 1st class master degree in relevant subjects from a recognized university with 4 years experience<br />OR<br />2nd class M.Sc + Ph.D degree in relevant subjects from a recognized university with 4 years experience.Desirable Qualification: Candidates should possess a PhD degree in any field of science.<br />Preference will be given to those who have published scientific papers in international journals and who have a track record of working in infectious diseases.</p>

<p>The candidate must know the following for further consideration: (a) data processing and analysis using statistical softwares, (d) programming, (e) presentation of complex data from excel files and related skills.<br />Understanding of GIS and malaria will be an advantage. Experience and interest in functional genomics and genomic sequencing will be important.</p>

<p>Age Limit: 40 YearsDuration: 30.09.2021</p>

<p>More at http://onlineapply.nimr.org.in/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43705/ognmconformational-dynamics-based-on-contact-topology-in-a-coarse-grained-presentation</guid>
	<pubDate>Mon, 17 Jan 2022 03:52:51 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43705/ognmconformational-dynamics-based-on-contact-topology-in-a-coarse-grained-presentation</link>
	<title><![CDATA[oGNM:Conformational dynamics based on contact topology in a coarse-grained presentation]]></title>
	<description><![CDATA[<p><a href="https://dyn.life.nthu.edu.tw/oGNM/Theory_GNM.php">Gaussian Network Model (GNM</a><span>) is a powerful tool to sample conformational dynamics based on contact topology in a coarse-grained presentation. Here we present a method to consider protein dynamics in the presence of &lsquo;environment&rsquo; (1). The &lsquo;environment&rsquo; here can be crystal contacts defined in structures solved by x-ray crystallography, a protein in homo-/hetero-dimers, a part of a protein complex, the DNA in complexed with transcription factors, or even a large ligand (or ligands) in a protein. The protein dynamics, in the presence of these &lsquo;environments&rsquo;, can be assessed in a more rigorous physics ground (the size and number of the orthogonal normal modes are the same as those in unperturbed systems (in the absence of the environment)) with our theories (2) that guarantee our implementations to be more efficient (saving 3/4 time, assuming equal size of system and environment), more memory friendly (saving &gt;1/2 time) and more accurate (enhanced correlation between predictions and B-factors). The environment consideration in ANM theory was published (1) and reviewed (2); its GNM counterpart is first derived in this work and proven to be more accurate in the B-factor predictions than conventional GNM.</span></p><p>Address of the bookmark: <a href="https://dyn.life.nthu.edu.tw/oGNM/oGNM.php" rel="nofollow">https://dyn.life.nthu.edu.tw/oGNM/oGNM.php</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41209/juicebox-visualization-and-analysis-software-for-hi-c-data</guid>
	<pubDate>Fri, 21 Feb 2020 00:33:38 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41209/juicebox-visualization-and-analysis-software-for-hi-c-data</link>
	<title><![CDATA[Juicebox: Visualization and analysis software for Hi-C data]]></title>
	<description><![CDATA[<p>Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox,&nbsp;<a href="https://github.com/theaidenlab/juicer/wiki/Download">Juicer Tools</a>, and&nbsp;<a href="https://aidenlab.org/assembly/">Assembly Tools</a>.&nbsp;<a href="https://github.com/theaidenlab/juicebox/wiki/Download">Download Juicebox here</a>, or use&nbsp;<a href="https://aidenlab.org/juicebox">Juicebox on the web</a>. Detailed documentation is available&nbsp;<a href="https://github.com/theaidenlab/juicebox/wiki">on the wiki</a>. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files.</p>
<p>Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website&nbsp;<a href="https://aidenlab.org/assembly">https://aidenlab.org/assembly</a>&nbsp;for more details on how to use Juicebox for assembly.</p>
<p>GUI at&nbsp;<a href="https://aidenlab.org/juicebox/">https://aidenlab.org/juicebox/</a></p><p>Address of the bookmark: <a href="https://github.com/aidenlab/Juicebox" rel="nofollow">https://github.com/aidenlab/Juicebox</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<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/41814/gggenes-a-ggplot2-extension-for-drawing-gene-arrow-maps</guid>
	<pubDate>Tue, 02 Jun 2020 11:43:34 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41814/gggenes-a-ggplot2-extension-for-drawing-gene-arrow-maps</link>
	<title><![CDATA[gggenes: a ggplot2 extension for drawing gene arrow maps.]]></title>
	<description><![CDATA[<p>Install the stable version of gggenes from CRAN:</p>
<p><code><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages("gggenes")</a></code></p>
<p>If you want the development version, install it from GitHub:</p>
<p><code><a href="https://www.rdocumentation.org/packages/devtools/topics/reexports">devtools::install_github("wilkox/gggenes")</a></code></p>
<p>More at&nbsp;<a href="https://github.com/wilkox/gggenes">https://github.com/wilkox/gggenes</a></p><p>Address of the bookmark: <a href="http://wilkox.org/gggenes" rel="nofollow">http://wilkox.org/gggenes</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43427/ogdraw-draw-organelle-genome-maps</guid>
	<pubDate>Tue, 05 Oct 2021 03:34:35 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43427/ogdraw-draw-organelle-genome-maps</link>
	<title><![CDATA[OGDRAW - Draw Organelle Genome Maps]]></title>
	<description><![CDATA[<p>OrganellarGenomeDRAW converts annotations in the&nbsp;<a href="https://www.ncbi.nlm.nih.gov/genbank/">GenBank</a>&nbsp;or&nbsp;<a href="https://www.ebi.ac.uk/ena">EMBL/ENA</a>&nbsp;format into graphical maps. The input has to be a&nbsp;<a href="https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html">GenBank&nbsp;</a>or&nbsp;<a href="https://www.ebi.ac.uk/ena/submit/flat-file">EMBL/ENA flat file</a>&nbsp;wherase the output can vary among several types of files. The application is optimized to create detailed high-quality maps of organellar genomes (plastid and mitochondria). Nevertheless, you can upload most<span style="color: #0b0118;">&nbsp;database</span>&nbsp;entries.</p>
<p>&nbsp;</p>
<p>Please take a look at our&nbsp;<a href="https://chlorobox.mpimp-golm.mpg.de/OGDraw-FAQ.html">FAQ section</a>&nbsp;and do not hesitate to report bugs or suggestions for improvements by&nbsp;<a href="mailto:chlorobox@mpimp-golm.mpg.de?subject=OGDRAW">email</a>.</p><p>Address of the bookmark: <a href="https://chlorobox.mpimp-golm.mpg.de/OGDraw.html" rel="nofollow">https://chlorobox.mpimp-golm.mpg.de/OGDraw.html</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32129/lordec-a-hybrid-error-correction-program-for-long-pacbio-reads</guid>
	<pubDate>Mon, 10 Apr 2017 04:16:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32129/lordec-a-hybrid-error-correction-program-for-long-pacbio-reads</link>
	<title><![CDATA[LoRDEC: a hybrid error correction program for long, PacBio reads]]></title>
	<description><![CDATA[<p>LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and the PacBio read set, which is then corrected using the reference set. Typically, the reference set contains Illumina reads.</p>
<p><br> Usually, errors in PacBio reads include many insertions and deletions, and comparatively less substitutions. LoRDEC can correct errors of all these types.<br> After correction, a larger portion of the sequence of PacBio reads is usable for detection of region of similarity with other sequences, for aligning them to the contigs of an assembly, etc.</p>
<p>Why is LoRDEC different?</p>
<ul>
<li>It is efficient and can process large read data sets, included from eukaryotic or vertebrate species, on a usual computing server, and even works on desktop/laptop computers.</li>
<li>It adopts a novel graph based approach: it builds a succinct De Bruijn Graph (DBG) representing the short reads, and seeks a corrective sequence for each erroneous region of a long read by traversing chosen paths in the graph.</li>
</ul><p>Address of the bookmark: <a href="http://www.atgc-montpellier.fr/lordec/" rel="nofollow">http://www.atgc-montpellier.fr/lordec/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33223/tbl2asn-a-command-line-program-that-automates-the-creation-of-sequence-records-for-submission-to-genbank</guid>
	<pubDate>Mon, 29 May 2017 07:37:08 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33223/tbl2asn-a-command-line-program-that-automates-the-creation-of-sequence-records-for-submission-to-genbank</link>
	<title><![CDATA[Tbl2asn: a command-line program that automates the creation of sequence records for submission to GenBank]]></title>
	<description><![CDATA[<p>Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank. Additional manual editing is not required before submission.</p>
<p>Tbl2asn is available by anonymous&nbsp;<a href="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/">FTP</a>. Copy the right version for your platform, then uncompress the file, rename it to "tbl2asn", and set the permissions, as necessary for the platform.</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/" rel="nofollow">https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
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