Words similar to dbest
Example sentences for: dbest
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The features in descending ranking were: UTRs based on known UTR indices; exons containing no ORFs or incomplete ORFs; boundaries of known full-length cDNAs (HTDB-based indices); EST orientation information (5' or 3' origin from the original IMAGE, UniGene/HINT, and dbEST databases); and Genscan-predicted poly(A) signals.
Following gel image analysis and DNA sequence extraction, sequence data were processed in an automated pipeline to: assess EST quality; trim flanking vector sequences; mask repetitive elements; remove contaminated ESTs; identify similarities by BLAST; identify cloning artifacts; and determine which portion of the EST to submit [ 83 ] . The resulting sequences were annotated with similarity information and sequence quality information and submitted to dbEST.
Following clustering, comparative analyses were performed using WU-BLASTX and WU-TBLASTX [ 92 93 ] with 1,798 contig consensus sequences (themselves grouped into 1,625 cluster groups) as queries versus multiple databases including SWIR v.21 (5/19/2000) non-redundant protein database and Wormpep v.54 C. elegans protein database (Wellcome Trust Sanger Institute, unpublished work), C. elegans mitochondrial protein sequences, and six internally constructed databases using intersections of data from the GenBank nucleotide database and dbEST [ 96 ] . These include: nemnoele (all nucleotide data from the phylum Nematoda with C. elegans removed); nemnoelenomi (nemnoele with M. incognita removed); nemnoelenomel (nemnoele with all Meloidogyne species removed); nemnoelenotyl (nemnoele with all Tylenchida species removed); yestylnomel (all Tylenchida species except Meloidogyne ); mj (only M. javanica sequences).
Databases: protein and nucleotide databases including dbest (ESTs), dsts (STSs) and htgs (unfinished high throughput genomic sequences)
Presently, nearly four million ESTs (dbEST release 04/19/02) are catalogued in dbEST representing about 80% or more of all human genes with at least one representative entry [ 15 ] . While not every gene is accounted for in dbEST, computer database searching, also known as in silico cloning, can identify new genes without actual physically manipulating DNA.
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