Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data.
BACKGROUND
DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.


BACKGROUND
GenSeed is available under the GNU General Public License at http://www.coccidia.icb.usp.br/genseed/
Sobreira
Tiago J P
TJ
Instituto do Coração - USP, Av. Prof. Enéas de Carvalho Aguiar 44, São Paulo SP, 05403-000, Brazil.
Gruber
Arthur
A
D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D003628:Database Management Systems; D030541:Databases, Genetic; D008969:Molecular Sequence Data; D020543:Proteome / Q000737:chemistry* / Q000235:genetics*; D017421:Sequence Analysis / Q000379:methods*
D020543:Proteome; D004247:DNA