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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/36921?offset=20</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35899/reference-free-prediction-of-rearrangement-breakpoint-reads</guid>
	<pubDate>Thu, 08 Mar 2018 05:05:25 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35899/reference-free-prediction-of-rearrangement-breakpoint-reads</link>
	<title><![CDATA[Reference-free prediction of rearrangement breakpoint reads]]></title>
	<description><![CDATA[<p><span>lideSort-BPR (&nbsp;</span><span>b</span><span>&nbsp;reak&nbsp;</span><span>p</span><span>&nbsp;oint&nbsp;</span><span>r</span><span>&nbsp;eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing depth of 100&times;, it finds &sim;88% of the breakpoints correctly with no false-positive reads. Moreover, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion transcripts correctly than previous approaches, and yet produces fewer false-positive reads. To our knowledge, this is the first method to detect breakpoint reads without using a reference genome.</span></p>
<p><span>https://github.com/ewijaya/slidesort-bpr</span></p><p>Address of the bookmark: <a href="https://code.google.com/archive/p/slidesort-bpr/" rel="nofollow">https://code.google.com/archive/p/slidesort-bpr/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads</guid>
	<pubDate>Tue, 08 May 2018 04:27:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads</link>
	<title><![CDATA[HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads]]></title>
	<description><![CDATA[<p><strong>HISAT2</strong><span>&nbsp;is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs&nbsp;</span><a href="http://dl.acm.org/citation.cfm?id=2674828">[Sir&eacute;n et al. 2014]</a><span>, we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).&nbsp;</span></p>
<p><span>more at&nbsp;https://ccb.jhu.edu/software/hisat2/index.shtml</span></p><p>Address of the bookmark: <a href="https://github.com/infphilo/hisat2" rel="nofollow">https://github.com/infphilo/hisat2</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/26456/the-mills-lab</guid>
  <pubDate>Wed, 24 Feb 2016 16:18:38 -0600</pubDate>
  <link></link>
  <title><![CDATA[The Mills lab]]></title>
  <description><![CDATA[
<p>The laboratory is focused on the discovery and analysis of structural variation (SVs) from genomic sequence data. As part of the 1000 Genomes Project and other endeavors, we have helped produce initial fine-scale maps using a variety of SV discovery approaches including: (i) paired-end mapping (or read pair analysis) based on abnormally mapped pairs of clone ends; (ii) read-depth analysis, which detects deletions and duplications through analysis of the read depth-of-coverage; (iii) split read analysis, which detects SVs by evaluating gapped sequence alignments; and (iv) sequence assembly, which enables the discovery of novel (non-reference) sequence insertions.</p>

<p>http://millslab.org/research.html</p>
]]></description>
</item>
<item>
	<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/bookmarks/view/40703/%CF%80-cyc-a-reference-free-snp-discovery-application-using-parallel-graph-search</guid>
	<pubDate>Tue, 28 Jan 2020 03:34:23 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40703/%CF%80-cyc-a-reference-free-snp-discovery-application-using-parallel-graph-search</link>
	<title><![CDATA[Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search]]></title>
	<description><![CDATA[<p>Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only</p>
<p><span>Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be unpractical for large error prone genomes which makes the assembly process produce an excessive number of false positive cycles.&nbsp; Our solution is to search the graph in multicores shared memory parallel mode using graph decomposition then use filtering method to generate good quality SNPs.</span></p>
<p><a href="https://arxiv.org/abs/1809.06700">https://arxiv.org/abs/1809.06700</a></p>
<p><a href="https://github.com/redayounsi/2KP2P">https://github.com/redayounsi/2KP2P</a></p>
<blockquote>
<p>/2kp2omp/bin/main_2kp2_K63_C2 -i fastq_files.txt -o fungus_bub.fasta -r stat_fungus.txt -c cov_fungus_hash.txt -k 63 -h 20 -b 100 -g 600 -l 100 -f 16 -t 5.0 -x 1 -v 0 -p 1 -y 1 -u 1</p>
<p>&nbsp;</p>
</blockquote><p>Address of the bookmark: <a href="https://github.com/redayounsi/2KP2P" rel="nofollow">https://github.com/redayounsi/2KP2P</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38752/hgtector-an-automated-method-facilitating-genome-wide-discovery-of-putative-horizontal-gene-transfers</guid>
	<pubDate>Mon, 21 Jan 2019 06:50:05 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38752/hgtector-an-automated-method-facilitating-genome-wide-discovery-of-putative-horizontal-gene-transfers</link>
	<title><![CDATA[HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers]]></title>
	<description><![CDATA[<p>A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics</p>
<p>Authors: Qiyun Zhu (<a href="mailto:qiyunzhu@gmail.com">qiyunzhu@gmail.com</a>), Katharina Dittmar (<a href="mailto:katharinad@gmail.com">katharinad@gmail.com</a>)</p>
<p>Affiliation: Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, USA</p>
<p>Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers.&nbsp;<em style="font-size: 12.8px;">BMC Genomics</em>. 2014. 15:717.</p>
<p>Usage: Simply execute&nbsp;<span style="font-size: 12.8px;">perl HGTector.pl</span>, or, open&nbsp;<span style="font-size: 12.8px;">GUI.html</span>&nbsp;in a web browser to see a step-by-step wizard.</p>
<p>Download&nbsp;<a href="https://github.com/DittmarLab/HGTector/archive/0.2.2.zip">HGTector 0.2.2</a>.</p><p>Address of the bookmark: <a href="https://github.com/DittmarLab/HGTector" rel="nofollow">https://github.com/DittmarLab/HGTector</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42965/nucl2vec-local-alignment-of-dna-sequences-using-distributed-vector-representation</guid>
	<pubDate>Tue, 16 Mar 2021 05:45:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42965/nucl2vec-local-alignment-of-dna-sequences-using-distributed-vector-representation</link>
	<title><![CDATA[Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation]]></title>
	<description><![CDATA[<p><span>We demonstrate a novel approach for</span><span>local alignment of DNA reads with respect to reference genome.</span><span>For this process we have used Skip-gram model for creating</span><span>encoding(Nucl2Vec) and k-nearest neighbor for the alignment.</span><span>With our new approach we have reduced computation cost for</span><span>local alignment , while achieving accuracy comparable to existing</span><span>defacto standard BWA-MEM tool.</span> </p>
<p><em>https://prakharg24.github.io/papers/401851.full.pdf</em></p><p>Address of the bookmark: <a href="https://prakharg24.github.io/papers/401851.full.pdf" rel="nofollow">https://prakharg24.github.io/papers/401851.full.pdf</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37606/stellar-fast-and-exact-local-alignments</guid>
	<pubDate>Wed, 29 Aug 2018 16:00:46 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37606/stellar-fast-and-exact-local-alignments</link>
	<title><![CDATA[STELLAR: fast and exact local alignments]]></title>
	<description><![CDATA[<p><span>STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at&nbsp;</span><span><a href="http://www.seqan.de/projects/stellar"><span>http://www.seqan.de/projects/stellar</span></a></span><span>.&nbsp;</span></p><p>Address of the bookmark: <a href="http://www.seqan.de/apps/stellar/" rel="nofollow">http://www.seqan.de/apps/stellar/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39200/omtools-a-software-package-for-visualizing-and-processing-optical-mapping-data</guid>
	<pubDate>Fri, 29 Mar 2019 01:21:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39200/omtools-a-software-package-for-visualizing-and-processing-optical-mapping-data</link>
	<title><![CDATA[OMTools: a software package for visualizing and processing optical mapping data]]></title>
	<description><![CDATA[<p><span>OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form an accessible and convenient pipeline for optical mapping analyses.</span></p>
<p><span><a href="https://github.com/TF-Chan-Lab/OMTools">https://github.com/TF-Chan-Lab/OMTools</a></span></p><p>Address of the bookmark: <a href="https://github.com/TF-Chan-Lab/OMTools" rel="nofollow">https://github.com/TF-Chan-Lab/OMTools</a></p>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26587/last</guid>
	<pubDate>Wed, 09 Mar 2016 14:27:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26587/last</link>
	<title><![CDATA[LAST]]></title>
	<description><![CDATA[<p style="text-align: center;"><img src="http://last.cbrc.jp/lastwebfig.png" alt="sketch of  similar regions in sequences" style="border: 0px;"></p>
<p>LAST can:</p>
<ul>
<li>Handle <strong>big</strong> sequence data, e.g:
<ul>
<li>Compare two vertebrate genomes</li>
<li>Align billions of DNA reads to a genome</li>
</ul>
</li>
<li>Indicate the <a href="http://lastweb.cbrc.jp/about.html">reliability</a> of each aligned column.</li>
<li>Use sequence quality data <a href="http://nar.oxfordjournals.org/content/38/7/e100.abstract">properly</a>.</li>
<li>Compare DNA to proteins, with frameshifts.</li>
<li>Compare PSSMs to sequences</li>
<li>Calculate the likelihood of chance similarities between random sequences.</li>
<li>Do split and spliced alignment.</li>
<li><a href="http://last.cbrc.jp/doc/last-train.html">Train</a> alignment parameters for unusual kinds of sequence (e.g. nanopore).</li>
</ul><p>Address of the bookmark: <a href="http://last.cbrc.jp/" rel="nofollow">http://last.cbrc.jp/</a></p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
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