ArticleNucleic acids research2011
SyMAP v3.4: a turnkey synteny system with application to plant genomes.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 190 papers.
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190 citing papers in PubMed.
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- Genomic hotspots of chromosome rearrangements explain conserved synteny despite high rates of chromosome evolution in a holocentric lineage.Molecular ecology · 2024Article
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130 more citing papers are in PubMed but not listed here.
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3 authors.
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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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