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SyMAP v3.4: a turnkey synteny system with application to plant genomes.

Soderlund C, Bomhoff M, Nelson WM - Nucleic Acids Res. (2011)

Bottom Line: These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice.The software may be used from a website or standalone for the best performance.A project manager is provided to organize and automate the analysis of multi-genome groups.

View Article: PubMed Central - PubMed

Affiliation: BIO5 Institute, 1657 Helen Street, University of Arizona, Tucson, AZ 85721, USA. cari@agcol.arizona.edu

ABSTRACT
SyMAP (Synteny Mapping and Analysis Program) was originally developed to compute synteny blocks between a sequenced genome and a FPC map, and has been extended to support pairs of sequenced genomes. SyMAP uses MUMmer to compute the raw hits between the two genomes, which are then clustered and filtered using the optional gene annotation. The filtered hits are input to the synteny algorithm, which was designed to discover duplicated regions and form larger-scale synteny blocks, where intervening micro-rearrangements are allowed. SyMAP provides extensive interactive Java displays at all levels of resolution along with simultaneous displays of multiple aligned pairs. The synteny blocks from multiple chromosomes may be displayed in a high-level dot plot or three-dimensional view, and the user may then drill down to see the details of a region, including the alignments of the hits to the gene annotation. These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice. The software may be used from a website or standalone for the best performance. A project manager is provided to organize and automate the analysis of multi-genome groups. The software is freely distributed at http://www.agcol.arizona.edu/software/symap.

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Related in: MedlinePlus

SyMAP region 2D view. Any region can be zoomed by dragging the mouse over the region in any of the chromosomes. The genes are represented in blue in the middle of each chromosome, where the thicker parts are exons. The brown bars represent the MUMmer anchors, where the light brown portions link clustered anchors. The yellow bars with text on the left are from the attributes field in the GFF file for maize, where the underlined text is an URL. The sizes of the regions are shown at the bottom of rice-1 (87 kb), maize-3 (281 kb) and maize-8 (497 kb). The three columns of arrows indicate sets of shared genes, as discussed in the text.
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Figure 4: SyMAP region 2D view. Any region can be zoomed by dragging the mouse over the region in any of the chromosomes. The genes are represented in blue in the middle of each chromosome, where the thicker parts are exons. The brown bars represent the MUMmer anchors, where the light brown portions link clustered anchors. The yellow bars with text on the left are from the attributes field in the GFF file for maize, where the underlined text is an URL. The sizes of the regions are shown at the bottom of rice-1 (87 kb), maize-3 (281 kb) and maize-8 (497 kb). The three columns of arrows indicate sets of shared genes, as discussed in the text.

Mentions: After duplications, one copy of the duplicated gene is often lost (45), which is very apparent when zooming in to various regions of Figure 3a, where one such region is shown in Figure 4. Two genes only occur between rice-1 and maize-3, four genes occur on all three chromosomes, and three genes only occur between rice-1 and maize-8 (shown in Figure 4 as the three columns of arrows, respectively). All anchor points but one are within annotations, where the small red arrow indicates the omission on maize-8.Figure 4.


SyMAP v3.4: a turnkey synteny system with application to plant genomes.

Soderlund C, Bomhoff M, Nelson WM - Nucleic Acids Res. (2011)

SyMAP region 2D view. Any region can be zoomed by dragging the mouse over the region in any of the chromosomes. The genes are represented in blue in the middle of each chromosome, where the thicker parts are exons. The brown bars represent the MUMmer anchors, where the light brown portions link clustered anchors. The yellow bars with text on the left are from the attributes field in the GFF file for maize, where the underlined text is an URL. The sizes of the regions are shown at the bottom of rice-1 (87 kb), maize-3 (281 kb) and maize-8 (497 kb). The three columns of arrows indicate sets of shared genes, as discussed in the text.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105427&req=5

Figure 4: SyMAP region 2D view. Any region can be zoomed by dragging the mouse over the region in any of the chromosomes. The genes are represented in blue in the middle of each chromosome, where the thicker parts are exons. The brown bars represent the MUMmer anchors, where the light brown portions link clustered anchors. The yellow bars with text on the left are from the attributes field in the GFF file for maize, where the underlined text is an URL. The sizes of the regions are shown at the bottom of rice-1 (87 kb), maize-3 (281 kb) and maize-8 (497 kb). The three columns of arrows indicate sets of shared genes, as discussed in the text.
Mentions: After duplications, one copy of the duplicated gene is often lost (45), which is very apparent when zooming in to various regions of Figure 3a, where one such region is shown in Figure 4. Two genes only occur between rice-1 and maize-3, four genes occur on all three chromosomes, and three genes only occur between rice-1 and maize-8 (shown in Figure 4 as the three columns of arrows, respectively). All anchor points but one are within annotations, where the small red arrow indicates the omission on maize-8.Figure 4.

Bottom Line: These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice.The software may be used from a website or standalone for the best performance.A project manager is provided to organize and automate the analysis of multi-genome groups.

View Article: PubMed Central - PubMed

Affiliation: BIO5 Institute, 1657 Helen Street, University of Arizona, Tucson, AZ 85721, USA. cari@agcol.arizona.edu

ABSTRACT
SyMAP (Synteny Mapping and Analysis Program) was originally developed to compute synteny blocks between a sequenced genome and a FPC map, and has been extended to support pairs of sequenced genomes. SyMAP uses MUMmer to compute the raw hits between the two genomes, which are then clustered and filtered using the optional gene annotation. The filtered hits are input to the synteny algorithm, which was designed to discover duplicated regions and form larger-scale synteny blocks, where intervening micro-rearrangements are allowed. SyMAP provides extensive interactive Java displays at all levels of resolution along with simultaneous displays of multiple aligned pairs. The synteny blocks from multiple chromosomes may be displayed in a high-level dot plot or three-dimensional view, and the user may then drill down to see the details of a region, including the alignments of the hits to the gene annotation. These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice. The software may be used from a website or standalone for the best performance. A project manager is provided to organize and automate the analysis of multi-genome groups. The software is freely distributed at http://www.agcol.arizona.edu/software/symap.

Show MeSH
Related in: MedlinePlus