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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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SyMAP chromosome 2D view. (a) Three chromosomes in 2D. (b) Two chromosomes in 2D. These two displays show the effect of transitive homology, where there is more homology via rice-1 than directly between maize-3 and maize-8. Each brown line represents an anchor. The size of the displayed region is shown at the lower end of the chromosome.
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Figure 3: SyMAP chromosome 2D view. (a) Three chromosomes in 2D. (b) Two chromosomes in 2D. These two displays show the effect of transitive homology, where there is more homology via rice-1 than directly between maize-3 and maize-8. Each brown line represents an anchor. The size of the displayed region is shown at the lower end of the chromosome.

Mentions: For a detailed view of maize-3 and maize-8 aligned to rice-1, all chromosomes were deselected except these two, then the 2D button was selected, which results in the view shown in Figure 3a. This view provides the most detail, where the large inversions and translocations are easy to see, and small changes can be viewed when zooming into a region. There is a large difference in the sizes of the chromosomes, where maize-3 is 230 Mb, rice-1 is 43 Mb and maize-8 is 174 Mb. This difference in size is only obvious by looking at the size at the bottom of each chromosome; however, the displayed regions may be drawn to scale using the SyMAP scale button (Supplementary Figure S3).Figure 3.


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

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

SyMAP chromosome 2D view. (a) Three chromosomes in 2D. (b) Two chromosomes in 2D. These two displays show the effect of transitive homology, where there is more homology via rice-1 than directly between maize-3 and maize-8. Each brown line represents an anchor. The size of the displayed region is shown at the lower end of the chromosome.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: SyMAP chromosome 2D view. (a) Three chromosomes in 2D. (b) Two chromosomes in 2D. These two displays show the effect of transitive homology, where there is more homology via rice-1 than directly between maize-3 and maize-8. Each brown line represents an anchor. The size of the displayed region is shown at the lower end of the chromosome.
Mentions: For a detailed view of maize-3 and maize-8 aligned to rice-1, all chromosomes were deselected except these two, then the 2D button was selected, which results in the view shown in Figure 3a. This view provides the most detail, where the large inversions and translocations are easy to see, and small changes can be viewed when zooming into a region. There is a large difference in the sizes of the chromosomes, where maize-3 is 230 Mb, rice-1 is 43 Mb and maize-8 is 174 Mb. This difference in size is only obvious by looking at the size at the bottom of each chromosome; however, the displayed regions may be drawn to scale using the SyMAP scale button (Supplementary Figure S3).Figure 3.

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