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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">MGAviewer: a desktop visualization tool for analysis of metagenomics
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></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23044549</idno><idno type="pmc">3530914</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530914</idno><idno type="RBID">PMC:3530914</idno><idno type="doi">10.1093/bioinformatics/bts567</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000497</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">MGAviewer: a desktop visualization tool for analysis of metagenomics
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></author></analytic><series><title level="j">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1367-4811</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abeel, T" uniqKey="Abeel T">T Abeel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bao, H" uniqKey="Bao H">H Bao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dreszer, Tr" uniqKey="Dreszer T">TR Dreszer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kent, Wj" uniqKey="Kent W">WJ Kent</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Manske, Hm" uniqKey="Manske H">HM Manske</name></author><author><name sortKey="Kwiatkowski, Dp" uniqKey="Kwiatkowski D">DP Kwiatkowski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mardis, Er" uniqKey="Mardis E">ER Mardis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Milne, I" uniqKey="Milne I">I Milne</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nicol, Jw" uniqKey="Nicol J">JW Nicol</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Niu, B" uniqKey="Niu B">B Niu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Popendorf, K" uniqKey="Popendorf K">K Popendorf</name></author><author><name sortKey="Sakakibara, Y" uniqKey="Sakakibara Y">Y Sakakibara</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, J" uniqKey="Qin J">J Qin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Robinson, Jt" uniqKey="Robinson J">JT Robinson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rusch, Db" uniqKey="Rusch D">DB Rusch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Skinner, Me" uniqKey="Skinner M">ME Skinner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sun, S" uniqKey="Sun S">S Sun</name></author></analytic></biblStruct></listBibl></div1></back></TEI><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></publisher></journal-meta><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
<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><body><sec id="SEC1"><title>1 INTRODUCTION</title><p>The advances of Next Generation Sequencing technologies (<xref ref-type="bibr" rid="bts567-B7">Mardis, 2011</xref>) have promoted big waves of metagenomic projects in
study of microbiomes under different environments such as ocean (<xref ref-type="bibr" rid="bts567-B14">Rusch <italic>et al.</italic>, 2007</xref>) and human body (<xref ref-type="bibr" rid="bts567-B12">Qin <italic>et al.</italic>, 2010</xref>). An essential
step in metagenomic data analysis is to align the sequencing reads against the available
microbial genomes.</p><p>Visualization is an intuitive way to analyze large-scale alignment data in genomic studies.
There are many visualization tools available. Some are web browser-based such as UCSC genome
browser (<xref ref-type="bibr" rid="bts567-B4">Dreszer <italic>et al.</italic>,
2012</xref>), LookSeq (<xref ref-type="bibr" rid="bts567-B6">Manske and Kwiatkowski,
2009</xref>) and JBrowse (<xref ref-type="bibr" rid="bts567-B15">Skinner <italic>et
al.</italic>, 2009</xref>). Some are standalone programs such as Tablet (<xref ref-type="bibr" rid="bts567-B8">Milne <italic>et al.</italic>, 2010</xref>), GenomeView
(<xref ref-type="bibr" rid="bts567-B1">Abeel <italic>et al.</italic>, 2012</xref>),
MapView (<xref ref-type="bibr" rid="bts567-B3">Bao <italic>et al.</italic>, 2009</xref>),
IGB (<xref ref-type="bibr" rid="bts567-B9">Nicol <italic>et al.</italic>, 2009</xref>), IGV
(<xref ref-type="bibr" rid="bts567-B13">Robinson <italic>et al.</italic>, 2011</xref>),
SamScope (<xref ref-type="bibr" rid="bts567-B11">Popendorf and Sakakibara, 2012</xref>) and
so on.</p><p>However, these sophisticated visualization tools are specialized in handling intraspecies
alignment results (i.e. query and reference are same species). They are not suitable for
interspecies alignments from metagenomic datasets, where query and reference can be from
different species. There are fundamental differences between intraspecies and interspecies
alignments. The former only involves one reference genome and represent features like single
nucleotide polymorphism and alternative splicing. But the latter involves multiple (often
10<sup>3</sup>) reference microbial genomes. To visualize interspecies alignments, a tool
needs to show the wide range of alignment similarities (100% to as low as 50%
for DNAs and 30% for proteins) and to handle thousands of reference genomes.</p><p>The Global Ocean Sampling study (<xref ref-type="bibr" rid="bts567-B14">Rusch <italic>et
al.</italic>, 2007</xref>) first introduced fragment recruitment plots to illustrate the
metagenomic alignment data. However, its underlying software is not available to the
public.</p><p>Here, we present MetaGenomic Alignment Viewer (MGAviewer), a platform-independent web
browser-based tool for visualizing alignment data. It does not rely on web server and
relational database for image generation and data retrieval. It can be simply used as a
standalone desktop program to analyze local data. It can also be included in a web server
like other web-based genome browsers.</p></sec><sec id="SEC2"><title>2 METHODS</title><p>The key component of this tool is a graphic interface with a 2D map that displays large
amounts of alignments between metagenomic sequences from one or more samples and a reference
genome (<xref ref-type="fig" rid="bts567-F1">Fig. 1</xref>). Users can explore alignment
data by interactively operating the 2D map in a similar way as in Google Maps. <fig id="bts567-F1" position="float"><label>Fig. 1.</label><caption><p>Screenshots of the MGAviewer
visualization interface</p></caption><graphic xlink:href="bts567f1"></graphic></fig></p><p>MGAviewer is an HTML5 web application. It works in all major modern browsers, including
Chrome, Firefox, Safari and Internet Explorer 9, without the need of installing any extra
software or plugin. It uses jQuery (<ext-link ext-link-type="uri" xlink:href="http://jquery.com/">http://jquery.com/</ext-link>) as the base JavaScript library, and on top of which, a
customized version of jQuery plotting plugin, Flot (<ext-link ext-link-type="uri" xlink:href="http://code.google.com/p/flot/">http://code.google.com/p/flot/</ext-link>). We extended Flot to make it support drawing
of fragments and annotation features. Above these, a site-specific JavaScript file
(‘site.js’) is responsible for setting up plot parameters, placing and
responding to additional controls and fetching data.</p><p>MGAviewer fetches alignment data from a user’s local computer or from a web server on
demand via AJAX. It then draws the plot in an HTML5 Canvas element. Every time a user
interaction event is triggered, e.g. zooming in/out, panning and resizing of the plot, the
plot image is simply redrawn using data already loaded, unless additional data are required.
This is in contrast to many other web-based genome browsers where plot images are generated
on the server side and then retrieved by browser on demand; in MGAviewer a plot is drawn
locally in browser. This results in no network traffic for most user operations and
therefore dramatically improves the responsiveness of user interactions, especially on slow
network.</p><p>Alignment data are stored in JSON (a lightweight data-interchange format used by
JavaScript) formatted files, which contain alignment details including coordinate, sequence
identity, name, e-value, etc. We provide scripts to generate JSON files from raw alignment
results by BLAST (<xref ref-type="bibr" rid="bts567-B2">Altschul <italic>et al.</italic>,
1997</xref>) and FR-HIT (<xref ref-type="bibr" rid="bts567-B10">Niu <italic>et
al.</italic>, 2011</xref>) and also from alignments in SAM format. These scripts need
installation of BioPython package. Converters for other programs like BLAT (<xref ref-type="bibr" rid="bts567-B5">Kent, 2002</xref>) can be easily implemented.</p><p>MGAviewer can be used as standalone software by simply opening the directory that contains
these JSON files, MGAviewer scripts and a master HTML file (see user’s guide for
details). It can also be hosted on a web server. The plot itself can be embedded in any
webpage.</p></sec><sec id="SEC3"><title>3 RESULTS</title><p>MGAviewer has an interface for users to select one or more metagenomic samples and a
reference from a list of reference genomes to generate the plot. The screenshots of
MGAviewer are shown in <xref ref-type="fig" rid="bts567-F1">Figure 1</xref>. The plot shows
alignments from eight metagenomic samples to a reference genome. The <italic>x</italic>-axis
is the genome coordinate, and <italic>y</italic>-axis is alignment identity (%).
Alignments are coloured by sample and are represented as points or lines depending on zoom
level. The bottom of the plot shows genes of the reference genome, and the top shows the
genome coverage for each sample. Icons at left and right bottom corners are for zoom, resize
and reset. Users can also zoom or pan the map by mouse. The inside circular images are
zoomed views of the plot.</p><p>We tested MGAviewer on 1.5 million alignment datasets between >600 metagenomic samples
from CAMERA (<xref ref-type="bibr" rid="bts567-B16">Sun <italic>et al.</italic>,
2011</xref>) and >2500 genomes from NCBI. MGAviewer provides real-time visualization for
almost all these datasets except a few hundred very large datasets, which need extra several
seconds for data loading and plotting. MGAviewer is already adopted by CAMERA project in its
alignment resources, which will be described in a separate publication. MGAviewer can be
used to analyze alignment data not only for prokaryotic species but also for viruses and
small eukaryotic organisms.</p><p><italic>Funding</italic>: This study was supported by Award
<award-id>R01HG005978</award-id> from the <funding-source>National Human Genome Research
Institute</funding-source> and the <funding-source>Gordon and Betty Moore
Foundation</funding-source>.</p><p><italic>Conflict of Interest</italic>: none declared.</p></sec></body><back><ref-list><title>References</title><ref id="bts567-B1"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Abeel</surname><given-names>T</given-names></name><etal></etal></person-group><article-title>GenomeView: a next-generation genome browser</article-title><source>Nucleic Acids Res.</source><year>2012</year><volume>40</volume><fpage>e12</fpage><pub-id pub-id-type="pmid">22102585</pub-id></element-citation></ref><ref id="bts567-B2"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Altschul</surname><given-names>SF</given-names></name><etal></etal></person-group><article-title>Gapped BLAST and PSI-BLAST: a new generation of protein database search
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|flux= Pmc
|étape= Corpus
|type= RBID
|clé=
|texte=
}}
| This area was generated with Dilib version V0.6.25. |  |