UVa FASTA Downloads

Latest news: 5 Jan 2007 : New search programs

Downloading and Installing FASTA3

Downloading Sequence Databases

Protein and DNA sequence library files can be downloaded from many different sources, including the NCBI and EMBL-EBI.

Database formats

The FASTA programs work with many different library formats; you will not need to run file conversion programs or formatting programs to search sequence libraries with FASTA. However, the FASTA programs assume that libraries are in FASTA format; to search libraries in other formats, the format type must be specified with the file name, e.g.
fasta34 -q mgstm1.aa "/slib/ncbi/refseq_protein 12"
would search the NCBI refseq_protein library in NCBI/BLAST formatdb format.

Supported popular library formats include:

FormatDescription
0 (or none) FASTA format
1 Genbank flatfile
3 EMBL-EBI/Swissprot flatfile
5 GCG/PIR flatfile
6 GCG compressed binary
12 NCBI BLAST formatdb version 2 (current version)
16 MySQL SQL query
17 PostgresQL SQL query