SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand
Identifieur interne : 000070 ( Main/Exploration ); précédent : 000069; suivant : 000071SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand
Auteurs : Haibao Tang [République populaire de Chine] ; Matthew D. Bomhoff ; Evan Briones ; Liangsheng Zhang [République populaire de Chine] ; James C. Schnable ; Eric LyonsSource :
- Genome Biology and Evolution [ 1759-6653 ] ; 2015.
Abstract
The identification of conserved syntenic regions enables discovery of predicted
locations for orthologous and homeologous genes, even when no such gene is present.
This capability means that synteny-based methods are far more effective than sequence
similarity-based methods in identifying true-negatives, a necessity for studying gene
loss and gene transposition. However, the identification of syntenic regions requires
complex analyses which must be repeated for pairwise comparisons between any two
species. Therefore, as the number of published genomes increases, there is a growing
demand for scalable, simple-to-use applications to perform comparative genomic
analyses that cater to both gene family studies and genome-scale studies. We
implemented SynFind, a web-based tool that addresses this need. Given one query
genome, SynFind is capable of identifying conserved syntenic regions in any set of
target genomes. SynFind is capable of reporting per-gene information, useful for
researchers studying specific gene families, as well as genome-wide data sets of
syntenic gene and predicted gene locations, critical for researchers focused on
large-scale genomic analyses. Inference of syntenic homologs provides the basis for
correlation of functional changes around genes of interests between related
organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic
data from over 15,000 organisms from all domains of life as well as supporting
multiple releases of the same organism. SynFind makes use of a powerful job execution
framework that promises scalability and reproducibility. SynFind can be accessed at
Url:
DOI: 10.1093/gbe/evv219
PubMed: 26560340
PubMed Central: 4700967
Affiliations:
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Le document en format XML
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<front><div type="abstract" xml:lang="en"><p>The identification of conserved syntenic regions enables discovery of predicted
locations for orthologous and homeologous genes, even when no such gene is present.
This capability means that synteny-based methods are far more effective than sequence
similarity-based methods in identifying true-negatives, a necessity for studying gene
loss and gene transposition. However, the identification of syntenic regions requires
complex analyses which must be repeated for pairwise comparisons between any two
species. Therefore, as the number of published genomes increases, there is a growing
demand for scalable, simple-to-use applications to perform comparative genomic
analyses that cater to both gene family studies and genome-scale studies. We
implemented SynFind, a web-based tool that addresses this need. Given one query
genome, SynFind is capable of identifying conserved syntenic regions in any set of
target genomes. SynFind is capable of reporting per-gene information, useful for
researchers studying specific gene families, as well as genome-wide data sets of
syntenic gene and predicted gene locations, critical for researchers focused on
large-scale genomic analyses. Inference of syntenic homologs provides the basis for
correlation of functional changes around genes of interests between related
organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic
data from over 15,000 organisms from all domains of life as well as supporting
multiple releases of the same organism. SynFind makes use of a powerful job execution
framework that promises scalability and reproducibility. SynFind can be accessed at
<ext-link ext-link-type="uri" xlink:href="http://genomevolution.org/CoGe/SynFind.pl">http://genomevolution.org/CoGe/SynFind.pl</ext-link>
. A video tutorial of SynFind
using <italic>Phytophthrora</italic>
as an example is available at <ext-link ext-link-type="uri" xlink:href="http://www.youtube.com/watch?v=2Agczny9Nyc">http://www.youtube.com/watch?v=2Agczny9Nyc</ext-link>
.</p>
</div>
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<biblStruct><analytic><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name>
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<author><name sortKey="Pedersen, B" uniqKey="Pedersen B">B Pedersen</name>
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<author><name sortKey="Freeling, M" uniqKey="Freeling M">M Freeling</name>
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<author><name sortKey="Tang, H" uniqKey="Tang H">H Tang</name>
</author>
<author><name sortKey="Freeling, M" uniqKey="Freeling M">M Freeling</name>
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<affiliations><list><country><li>République populaire de Chine</li>
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<tree><noCountry><name sortKey="Bomhoff, Matthew D" sort="Bomhoff, Matthew D" uniqKey="Bomhoff M" first="Matthew D." last="Bomhoff">Matthew D. Bomhoff</name>
<name sortKey="Briones, Evan" sort="Briones, Evan" uniqKey="Briones E" first="Evan" last="Briones">Evan Briones</name>
<name sortKey="Lyons, Eric" sort="Lyons, Eric" uniqKey="Lyons E" first="Eric" last="Lyons">Eric Lyons</name>
<name sortKey="Schnable, James C" sort="Schnable, James C" uniqKey="Schnable J" first="James C." last="Schnable">James C. Schnable</name>
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<country name="République populaire de Chine"><noRegion><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name>
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<name sortKey="Zhang, Liangsheng" sort="Zhang, Liangsheng" uniqKey="Zhang L" first="Liangsheng" last="Zhang">Liangsheng Zhang</name>
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