Biomedical Engineering Reference
In-Depth Information
READSEQ accepts and automatically recognizes 16 different input formats, including IG/Stanford,
GenBank/GB, NBRF, EMBL, Plain/Raw, Fitch, and Pearson/FASTA. Output formats include support for
the major formats, including ASN.1, EMBL, PAUP/NEXUS, DNAStrider, GenBank/GB, Phylip, and
IG/Stanford. READSEQ, like most file translation utilities, doesn't handle every format conversion.
This is in part due to the hundreds of application-specific file formats used in bioinformatics work.
Sequence Databases
The key protein sequence databases used for sequence alignment are SWISS-PROT, TrEMBL, and
PROSITE. These and other databases and tools are available through the ExPASy server of the Swiss
Institute of Bioinformatics. SWISS-PROT is a highly annotated protein sequence database that is
highly integrated with other databases in the ExPASy system. The TrEMBL database is a supplement
of SWISS-PROT that also contains translations of the EMBL nucleotide database that have not yet
been integrated into the latest official release of SWISS-PROT. PROSITE is a database of protein
families and domains that contains high-level profiles such as categories of toxins, inhibitors,
chaperone proteins, and hormones. The major source of nucleotide sequence data for alignment
research is NCBI's integrated Entrez system, which contains data from GenBank, RefSeq, and PDB.
BLOCKS is a database of ungapped multiple protein sequence alignments. Finally, SCOP, which
incorporates all PDB entries, is a structural classification database expressly designed for the
investigation of protein sequences and structures.
