---
name: "fastacmd"
section: "1"
platform: "linux"
package: "blast2"
version: "1:2.2.26.20120620-8"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastacmd"
---

# fastacmd(1)

retrieve FASTA sequences from a BLAST database

## NAME

fastacmd - retrieve FASTA sequences from a BLAST database

## SYNOPSIS

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

## DESCRIPTION

**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*

## OPTIONS

*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*

## EXIT STATUS

- 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.*

## AUTHOR

*The National Center for Biotechnology Information.*

## SEE ALSO

[**blast**(1)](/blast/1.md), */usr/share/doc/blast2/fastacmd.html.*