CyberinfraV1, Ncbi, Merge, bibRecord, 000358

MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data

Identifieur interne : 000358 ( Ncbi/Merge ); précédent : 000357; suivant : 000359

MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data

Auteurs : Zhengwei Zhu ; Beifang Niu ; Jing Chen ; Sitao Wu ; Shulei Sun ; Weizhong Li

Source :

Bioinformatics [ 1367-4803 ] ; 2012.

RBID : PMC:3530914

Abstract

Summary: Numerous metagenomics projects have produced tremendous amounts of sequencing data. Aligning these sequences to reference genomes is an essential analysis in metagenomics studies. Large-scale alignment data call for intuitive and efficient visualization tool. However, current tools such as various genome browsers are highly specialized to handle intraspecies mapping results. They are not suitable for alignment data in metagenomics, which are often interspecies alignments. We have developed a web browser-based desktop application for interactively visualizing alignment data of metagenomic sequences. This viewer is easy to use on all computer systems with modern web browsers and requires no software installation.

Availability:http://weizhongli-lab.org/mgaviewer

Contact:liwz@sdsc.edu

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530914

DOI: 10.1093/bioinformatics/bts567
PubMed: 23044549
PubMed Central: 3530914

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Le document en format XML

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alignment data</title>
<author><name sortKey="Zhu, Zhengwei" sort="Zhu, Zhengwei" uniqKey="Zhu Z" first="Zhengwei" last="Zhu">Zhengwei Zhu</name>
</author>
<author><name sortKey="Niu, Beifang" sort="Niu, Beifang" uniqKey="Niu B" first="Beifang" last="Niu">Beifang Niu</name>
</author>
<author><name sortKey="Chen, Jing" sort="Chen, Jing" uniqKey="Chen J" first="Jing" last="Chen">Jing Chen</name>
</author>
<author><name sortKey="Wu, Sitao" sort="Wu, Sitao" uniqKey="Wu S" first="Sitao" last="Wu">Sitao Wu</name>
</author>
<author><name sortKey="Sun, Shulei" sort="Sun, Shulei" uniqKey="Sun S" first="Shulei" last="Sun">Shulei Sun</name>
</author>
<author><name sortKey="Li, Weizhong" sort="Li, Weizhong" uniqKey="Li W" first="Weizhong" last="Li">Weizhong Li</name>
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<front><div type="abstract" xml:lang="en"><p><bold>Summary:</bold> Numerous metagenomics projects have produced tremendous amounts of
sequencing data. Aligning these sequences to reference genomes is an essential analysis in
metagenomics studies. Large-scale alignment data call for intuitive and efficient
visualization tool. However, current tools such as various genome browsers are highly
specialized to handle intraspecies mapping results. They are not suitable for alignment
data in metagenomics, which are often interspecies alignments. We have developed a web
browser-based desktop application for interactively visualizing alignment data of
metagenomic sequences. This viewer is easy to use on all computer systems with modern web
browsers and requires no software installation.</p>
<p><bold>Availability:</bold>
<ext-link ext-link-type="uri" xlink:href="http://weizhongli-lab.org/mgaviewer">http://weizhongli-lab.org/mgaviewer</ext-link>
</p>
<p><bold>Contact:</bold>
<email>liwz@sdsc.edu</email>
</p>
</div>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
  <front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">Bioinformatics</journal-id>
<journal-id journal-id-type="publisher-id">bioinformatics</journal-id>
<journal-id journal-id-type="hwp">bioinfo</journal-id>
<journal-title-group><journal-title>Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="ppub">1367-4803</issn>
<issn pub-type="epub">1367-4811</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
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<article-meta><article-id pub-id-type="pmid">23044549</article-id>
<article-id pub-id-type="pmc">3530914</article-id>
<article-id pub-id-type="doi">10.1093/bioinformatics/bts567</article-id>
<article-id pub-id-type="publisher-id">bts567</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Applications Note</subject>
<subj-group><subject>Sequence Analysis</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>MGAviewer: a desktop visualization tool for analysis of metagenomics
alignment data</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Zhu</surname>
<given-names>Zhengwei</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Niu</surname>
<given-names>Beifang</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Jing</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Wu</surname>
<given-names>Sitao</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Sun</surname>
<given-names>Shulei</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Weizhong</given-names>
</name>
<xref ref-type="corresp" rid="bts567-COR1">*</xref>
</contrib>
</contrib-group>
<aff>Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA</aff>
<author-notes><corresp id="bts567-COR1">*To whom correspondence should be addressed.</corresp>
<fn><p>Associate Editor: Alex Bateman</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>1</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>8</day>
<month>10</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>8</day>
<month>10</month>
<year>2012</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the 
 							. </pmc-comment>
      <volume>29</volume>
<issue>1</issue>
<fpage>122</fpage>
<lpage>123</lpage>
<history><date date-type="received"><day>9</day>
<month>3</month>
<year>2012</year>
</date>
<date date-type="rev-recd"><day>29</day>
<month>8</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>17</day>
<month>9</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2012. Published by Oxford University
Press.</copyright-statement>
<copyright-year>2012</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by/3.0"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0">http://creativecommons.org/licenses/by/3.0</ext-link>), which permits
unrestricted use, distribution, and reproduction in any medium, provided the original
work is properly cited.</license-p>
</license>
</permissions>
<abstract><p><bold>Summary:</bold> Numerous metagenomics projects have produced tremendous amounts of
sequencing data. Aligning these sequences to reference genomes is an essential analysis in
metagenomics studies. Large-scale alignment data call for intuitive and efficient
visualization tool. However, current tools such as various genome browsers are highly
specialized to handle intraspecies mapping results. They are not suitable for alignment
data in metagenomics, which are often interspecies alignments. We have developed a web
browser-based desktop application for interactively visualizing alignment data of
metagenomic sequences. This viewer is easy to use on all computer systems with modern web
browsers and requires no software installation.</p>
<p><bold>Availability:</bold>
<ext-link ext-link-type="uri" xlink:href="http://weizhongli-lab.org/mgaviewer">http://weizhongli-lab.org/mgaviewer</ext-link>
</p>
<p><bold>Contact:</bold>
<email>liwz@sdsc.edu</email>
</p>
</abstract>
<counts><page-count count="2"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Chen, Jing" sort="Chen, Jing" uniqKey="Chen J" first="Jing" last="Chen">Jing Chen</name>
<name sortKey="Li, Weizhong" sort="Li, Weizhong" uniqKey="Li W" first="Weizhong" last="Li">Weizhong Li</name>
<name sortKey="Niu, Beifang" sort="Niu, Beifang" uniqKey="Niu B" first="Beifang" last="Niu">Beifang Niu</name>
<name sortKey="Sun, Shulei" sort="Sun, Shulei" uniqKey="Sun S" first="Shulei" last="Sun">Shulei Sun</name>
<name sortKey="Wu, Sitao" sort="Wu, Sitao" uniqKey="Wu S" first="Sitao" last="Wu">Sitao Wu</name>
<name sortKey="Zhu, Zhengwei" sort="Zhu, Zhengwei" uniqKey="Zhu Z" first="Zhengwei" last="Zhu">Zhengwei Zhu</name>
</noCountry>
</tree>
</affiliations>
</record>

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MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data

MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data

Source :

Abstract

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