title: Management and visualization of whole genome shotgun assemblies using SAM.
abstract: We have designed and implemented a system to manage whole genome shotgun sequences and whole genome sequence assembly data flow. The Sequence Assembly Manager (SAM) consists primarily of a MySQL relational database and Perl applications designed to easily manipulate and coordinate the analysis of sequence information and to view and report genome assembly progress through its Common Gateway Interface (CGI) web interface. The application includes a tool to compare sequence assemblies to fingerprint maps that has been used successfully to improve and validate both maps and sequence assemblies of the Rhodococcus sp.RHAI and Cryptococcus neoformans WM276 genomes.
authors.affiliation: Genome Sciences Centre, Vancouver, BC, Canada.
authors.forename: René L
authors.initials: RL
authors.lastname: Warren
authors.forename: Yaron S
authors.initials: YS
authors.lastname: Butterfield
authors.forename: Ryan D
authors.initials: RD
authors.lastname: Morin
authors.forename: Asim S
authors.initials: AS
authors.lastname: Siddiqui
authors.forename: Marco A
authors.initials: MA
authors.lastname: Marra
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D016172:DNA Fingerprinting / Q000379:methods*; D030561:Databases, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface