Querying the public databases for sequences using complex keywords contained in the feature lines.

ABSTRACT:

Background

High throughput technologies often require the retrieval of large data sets of sequences. Retrieval of EMBL or GenBank entries using keywords is easy using tools such as ACNUC, Entrez or SRS, but has some limitations, in particular when querying with complex keywords.

Results

We show that Entrez has severe limitations with respect to retrieving subsequences. SRS works well with simple keywords but not with keywords composed of several terms, and has problems with complex queries. ACNUC works well, but does not allow precise queries in the Feature qualifiers. We developed specific Perl scripts to precisely retrieve subsequences as defined by complex descriptors in the Features qualifiers of the EMBL entries. We improved parts of the bioPerl library to allow parsing

SUBMITTER: Croce O 

PROVIDER: S-EPMC1403806 | biostudies-literature | 2006 Jan

REPOSITORIES: biostudies-literature