# The MEME Suite

## Motif-based sequence analysis tools

## fasta-grep

### Usage:

`fasta-grep <re> (-dna | -prot) [options]`

### Description

`fasta-grep` displays the non-overlapping occurrences of a PERL regular expression in FASTA sequences. `fasta-grep` supports the IUPAC alphabets for amino acids and nucleotides.

### Input

#### <re>

A PERL regular expression.

#### -dna | -prot

The sequences are DNA or protein, respectively.

Reads FASTA formatted sequences from standard input.

### Output

Writes matches to the regular expression to standard output or, optionally, a file. The output is in the form

            FASTA sequence ID line followed by number of matches
            [line 1 of sequence]
            [match line 1]
            [line 2 of sequence]
            [match line 2]
            ...
            [last line of sequence]
            [last match line]

For proteins, occurrences are marked on the match lines as:

            >    start of occurrence
            <    end of occurrence

For DNA, occurrences are marked on the match line as:

            >    start of occurrence
            <    end of occurrence
            *    start and end of two occurrences

### Options

Option | Parameter | Description | Default Behavior
--- | --- | --- | ---
General Options
-dna |  | Sequence is DNA. |
-prot |  | Sequence is protein. |
-s |  | Print whole matching sequences only. |
-p |  | Print positions only, not sequence; 1-based. (relative to input strand if DNA; see below) |
-m |  | Print IDs of matching sequences only. |
-x |  | Print IDs of non-matching sequences only. |
-o |  | Print occurrences only in "raw" format. |
-f |  | Print occurrences only in FASTA format. 1-based positions (relative to the strand of the match if DNA) are appended to the sequence ID. |
-a |  | Print all occurrences (even overlapping ones); ignored unless -o or -f given. |
-norc |  | Only print matches to given strand. | print matches for both DNA strands.
-prosite |  | <re> is in PROSITE format. | print matches for both DNA strands.
-erase |  | Replace occurrences with 'N's; DNA only. |

### Examples

        fasta-grep WGATAAN -dna < ~/crp0.s
        fasta-grep A[AT]G -dna < ~/crp0.fasta