fastacmd (1)

fastacmd [\|-\|] [\|-D N\|] [\|-I\|] [\|-L start,stop\|] [\|-P N\|] [\|-S N\|] [\|-T\|] [\|-a\|] [\|-c\|] [\|-d str\|] [\|-i str\|] [\|-l N\|] [\|-o filename\|] [\|-p type\|] [\|-s str\|] [\|-t\|]

fastacmd retrieves FASTA formatted sequences from a blast(1) database formatted using the `-o' option. An example fastacmd call would be

fastacmd -d nr -s p38398

A summary of options is included below.

-

Print usage message

-D N

Dump the entire database in some format:

1

fasta

2

GI list

3

Accession.version list

-I

Print database information only (overrides all other options)

-L start,stop

Range of sequence to extract (0 in start is beginning of sequence, 0 in stop is end of sequence, default is whole sequence)

-P N

Retrieve sequences with Protein Identification Group (PIG) N.

-S N

Strand on subsequence (nucleotide only):

1

top (default)

2

bottom

-T

Print taxonomic information for requested sequence(s)

-a

Retrieve duplicate accessions

-c

Use ^A (\001) as non-redundant defline separator

-d str

Database (default is nr)

-i str

Input file with GIs/accessions/loci for batch retrieval

-l N

Line length for sequence (default = 80)

-o filename

Output file (default = stdout)

-p type

Type of file:

G

guess (default): look for protein, then nucleotide

T

protein

F

nucleotide

-s str

Comma-delimited search string(s). GIs, accessions, loci, or fullSeq-id strings may be used, e.g., 555, AC147927, 'gnl|dbname|tag'

-t

Definition line should contain target GI only

0

Completed successfully.

1

An error (other than those below) occurred.

2

The BLAST database was not found.

3

A search (accession, GI, or taxonomy info) failed.

4

No taxonomy database was found.

The National Center for Biotechnology Information.

blast(1), /usr/share/doc/blast2/fastacmd.html.