UniBLAST and the EST Extractor: new WWW resources for EST data mining

Abstract

Expressed sequence tags (ESTs) are nucleotide sequences generated from the ends of randomly selected cDNA clones. More than 1 500 000 entries generated from different tissues and species are now stored in the public EST database (dbEST) maintained at the National Center for Biotechnology[1]. The NCBI periodically analyzes all human ESTs and sequences of known genes to identify and cluster the ones belonging to the same transcript. The result of this effort is stored in the UniGene database[2], which, as of March 1998, contained more than 39 000 clusters. Both dbESt and UniGene are available from the NCBI anonymous FTP server as downloadable flat data files. Exploiting these two databases, we developed two WWW applications, UniBLAST and the EST Extractor, which can be useful to researchers involved in positional cloning projects or interested in extending the sequence information associated with a single EST. UniBLast[3]is a non interactive BLAST search server that queries a formatted version of the UniGene database maintained at Tigem. Using UniBLast, a researcher can easily assess the number of UniGene clusters (and consequently the number of gene transcripts) similar to a query sequence in a single step. The UniGene database at Tigem is synchronized with the one provided by the NCBI. The EST Extractor[4]performs a remote interactive BLAST search (either a BLASTN or a TBLASTN analysis) versus dbEST at NCBI and reformats the search output, adding the following possibilities:•Manually selecting the significant EST hits from the search output.•Retrieving the selected EST sequences from dbEST at Tigem.•Displaying the links with UniGene entries, both from NCBI and Tigem.•Assembling or aligning the selected EST sequences, using the Cap2 assembler[5]or the ClustalW multiple alignment[6]programs.•Repeating either the whole EST Extractor procedure or performing a remote BLAST search at NCBI with a selected EST sequence contig generated by the assembly program.