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The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes.

Misra G, Priya P, Bandhiwal N, Bareja N, Jain M, Bhatia S, Chattopadhyay D, Tyagi AK, Yadav G - BMC Plant Biol. (2014)

Bottom Line: CGWR has been designed and configured for mapping, scanning and browsing the significant chickpea genomic features in view of the important existing and potential roles played by the various legume genome projects in mutant mapping and cloning.It is also the only plant based web resource supporting display and analysis of nucleosome positioning patterns in the genome.The usefulness of CGWR has been demonstrated with discoveries of biological significance made using this server.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Availability of the draft nuclear genome sequences of small-seeded desi-type legume crop Cicer arietinum has provided an opportunity for investigating unique chickpea genomic features and evaluation of their biological significance. The increasing number of legume genome sequences also presents a challenge for developing reliable and information-driven bioinformatics applications suitable for comparative exploration of this important class of crop plants.

Results: The Chickpea Genomic Web Resource (CGWR) is an implementation of a suite of web-based applications dedicated to chickpea genome visualization and comparative analysis, based on next generation sequencing and assembly of Cicer arietinum desi-type genotype ICC4958. CGWR has been designed and configured for mapping, scanning and browsing the significant chickpea genomic features in view of the important existing and potential roles played by the various legume genome projects in mutant mapping and cloning. It also enables comparative informatics of ICC4958 DNA sequence analysis with other wild and cultivated genotypes of chickpea, various other leguminous species as well as several non-leguminous model plants, to enable investigations into evolutionary processes that shape legume genomes.

Conclusions: CGWR is an online database offering a comprehensive visual and functional genomic analysis of the chickpea genome, along with customized maps and gene-clustering options. It is also the only plant based web resource supporting display and analysis of nucleosome positioning patterns in the genome. The usefulness of CGWR has been demonstrated with discoveries of biological significance made using this server. The CGWR is compatible with all available operating systems and browsers, and is available freely under the open source license at http://www.nipgr.res.in/CGWR/home.php.

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Related in: MedlinePlus

The Maps Tool of CGWR. This tool can be used for generating customized genome wide interactive maps of genes and gene families of interest. Six kinds of pre-generated maps are available, along with clustering options. Seamless integration with the chickpea genome browser as shown in the lower right panel enables further analysis.
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Fig4: The Maps Tool of CGWR. This tool can be used for generating customized genome wide interactive maps of genes and gene families of interest. Six kinds of pre-generated maps are available, along with clustering options. Seamless integration with the chickpea genome browser as shown in the lower right panel enables further analysis.

Mentions: Figure 4 shows a flowchart based outline of the Maps Tool in the CGWR. The ‘create your own map’ option allows users to paste the IDs of their desired set of gene models to visualize spatial location maps similar to the ones depicted in Figure 3. On the submission form, users can type the gene ID into the input box, and hit enter on the keyboard. An example set of gene IDs is provided within the form itself. Users can also determine the CIDs of genes of interest through the keyword search. As shown in Figure 4, the map tool returns a table listing out the loci, start and end positions of the specified gene IDs provided as input. At the top of this table is a link to view Map that leads to the mapped image. If the gene of interest lies on one of the unassembled scaffolds, rather than one of the eight pseudomolecules, the program assigns it to an independent unassembled unit or virtual LG termed as ‘UN’. An example of such a case is provided within the CGWR pre-generated maps. These custom generated maps are interactive, allowing users to click any region of interest on the map, to visualize details about the respective region as described in the previous section. In addition, users can directly find links to the chickpea browser from any of the input gene models mapped by this algorithm, as clicking on these links redirects users to the corresponding regions of the chickpea genome, as shown in Figure 4. These maps can also be downloaded as high-resolution images for publication purposes. Thus, the CGWR provides direct connection between its various features by connecting Tools, Maps and the Browser at its backend.Figure 4


The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes.

Misra G, Priya P, Bandhiwal N, Bareja N, Jain M, Bhatia S, Chattopadhyay D, Tyagi AK, Yadav G - BMC Plant Biol. (2014)

The Maps Tool of CGWR. This tool can be used for generating customized genome wide interactive maps of genes and gene families of interest. Six kinds of pre-generated maps are available, along with clustering options. Seamless integration with the chickpea genome browser as shown in the lower right panel enables further analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4307184&req=5

Fig4: The Maps Tool of CGWR. This tool can be used for generating customized genome wide interactive maps of genes and gene families of interest. Six kinds of pre-generated maps are available, along with clustering options. Seamless integration with the chickpea genome browser as shown in the lower right panel enables further analysis.
Mentions: Figure 4 shows a flowchart based outline of the Maps Tool in the CGWR. The ‘create your own map’ option allows users to paste the IDs of their desired set of gene models to visualize spatial location maps similar to the ones depicted in Figure 3. On the submission form, users can type the gene ID into the input box, and hit enter on the keyboard. An example set of gene IDs is provided within the form itself. Users can also determine the CIDs of genes of interest through the keyword search. As shown in Figure 4, the map tool returns a table listing out the loci, start and end positions of the specified gene IDs provided as input. At the top of this table is a link to view Map that leads to the mapped image. If the gene of interest lies on one of the unassembled scaffolds, rather than one of the eight pseudomolecules, the program assigns it to an independent unassembled unit or virtual LG termed as ‘UN’. An example of such a case is provided within the CGWR pre-generated maps. These custom generated maps are interactive, allowing users to click any region of interest on the map, to visualize details about the respective region as described in the previous section. In addition, users can directly find links to the chickpea browser from any of the input gene models mapped by this algorithm, as clicking on these links redirects users to the corresponding regions of the chickpea genome, as shown in Figure 4. These maps can also be downloaded as high-resolution images for publication purposes. Thus, the CGWR provides direct connection between its various features by connecting Tools, Maps and the Browser at its backend.Figure 4

Bottom Line: CGWR has been designed and configured for mapping, scanning and browsing the significant chickpea genomic features in view of the important existing and potential roles played by the various legume genome projects in mutant mapping and cloning.It is also the only plant based web resource supporting display and analysis of nucleosome positioning patterns in the genome.The usefulness of CGWR has been demonstrated with discoveries of biological significance made using this server.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Availability of the draft nuclear genome sequences of small-seeded desi-type legume crop Cicer arietinum has provided an opportunity for investigating unique chickpea genomic features and evaluation of their biological significance. The increasing number of legume genome sequences also presents a challenge for developing reliable and information-driven bioinformatics applications suitable for comparative exploration of this important class of crop plants.

Results: The Chickpea Genomic Web Resource (CGWR) is an implementation of a suite of web-based applications dedicated to chickpea genome visualization and comparative analysis, based on next generation sequencing and assembly of Cicer arietinum desi-type genotype ICC4958. CGWR has been designed and configured for mapping, scanning and browsing the significant chickpea genomic features in view of the important existing and potential roles played by the various legume genome projects in mutant mapping and cloning. It also enables comparative informatics of ICC4958 DNA sequence analysis with other wild and cultivated genotypes of chickpea, various other leguminous species as well as several non-leguminous model plants, to enable investigations into evolutionary processes that shape legume genomes.

Conclusions: CGWR is an online database offering a comprehensive visual and functional genomic analysis of the chickpea genome, along with customized maps and gene-clustering options. It is also the only plant based web resource supporting display and analysis of nucleosome positioning patterns in the genome. The usefulness of CGWR has been demonstrated with discoveries of biological significance made using this server. The CGWR is compatible with all available operating systems and browsers, and is available freely under the open source license at http://www.nipgr.res.in/CGWR/home.php.

Show MeSH
Related in: MedlinePlus