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

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

SUBMITTER: Soderlund C 

PROVIDER: S-EPMC3105427 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature