{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T20:41:10Z","timestamp":1760820070358},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: 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.<\/jats:p>\n               <jats:p>Availability: GenSeed is available under the GNU General Public License at http:\/\/www.coccidia.icb.usp.br\/genseed\/<\/jats:p>\n               <jats:p>Contact: \u00a0argruber@usp.br<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at http:\/\/www.coccidia.icb.usp.br\/genseed\/<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn283","type":"journal-article","created":{"date-parts":[[2008,6,11]],"date-time":"2008-06-11T00:13:53Z","timestamp":1213143233000},"page":"1676-1680","source":"Crossref","is-referenced-by-count":7,"title":["Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data"],"prefix":"10.1093","volume":"24","author":[{"given":"Tiago J. P.","family":"Sobreira","sequence":"first","affiliation":[{"name":"1 Instituto do Cora\u00e7\u00e3o - USP, Av. Prof. En\u00e9as de Carvalho Aguiar 44, Bloco 2, 10\u00b0 andar, S\u00e3o Paulo SP, 05403-000, Brazil and 2Departamento de Parasitologia, Instituto de Ci\u00eancias Biom\u00e9dicas, Universidade de S\u00e3o Paulo, S\u00e3o Paulo SP, 05508-000, Brazil"}]},{"given":"Arthur","family":"Gruber","sequence":"additional","affiliation":[{"name":"1 Instituto do Cora\u00e7\u00e3o - USP, Av. Prof. En\u00e9as de Carvalho Aguiar 44, Bloco 2, 10\u00b0 andar, S\u00e3o Paulo SP, 05403-000, Brazil and 2Departamento de Parasitologia, Instituto de Ci\u00eancias Biom\u00e9dicas, Universidade de S\u00e3o Paulo, S\u00e3o Paulo SP, 05508-000, Brazil"}]}],"member":"286","published-online":{"date-parts":[[2008,6,9]]},"reference":[{"key":"2023020210481574600_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023020210481574600_B2","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1093\/bioinformatics\/18.10.1396","article-title":"GENOTRACE: cDNA-based local GENOme assembly from TRACE archives","volume":"18","author":"Berezikov","year":"2002","journal-title":"Bioinformatics"},{"key":"2023020210481574600_B3","doi-asserted-by":"crossref","first-page":"34245","DOI":"10.1074\/jbc.M504158200","article-title":"Proteomic analysis of rhoptry organelles reveals many novel constituents for host-parasite interactions in Toxoplasma gondii","volume":"280","author":"Bradley","year":"2005","journal-title":"J. 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