glam2scan [options] <alphabet> <glam2 motif> <sequences>
The alphabet of the motif and sequences. This can be 'p' for protein sequences, 'n' for nucleotide sequences or the name of an GLAM2 alphabet file.
A file containing a GLAM2 motif. If the file contains multiple motifs
then GLAM2SCAN only considers the top one. The file may be either GLAM2's plain
text (glam2.txt) or HTML (glam2.html) output.
The minimal component of the GLAM2 motif is shown in this GLAM2 DNA motif and GLAM2 protein motif.
A file containing FASTA formatted sequences.
Outputs glam2scan.html and glam2scan.txt to the
selected directory.
(The HTML format contains slightly less information but is easier to read.)
Output begins with some general information stating the program name, version and the actual command line:
GLAM2scan
Version 9999
glam2scan p prot_motif.glam2 lotsa_prots.fa
This is followed by motif matches, sorted in order of score. A motif match looks like this:
| NAME | START | SITE | END | STRAND | SCORE |
|---|---|---|---|---|---|
| ****.*********..*********.*** | |||||
| At1g01140.2_SnRK3.12 | 196 | YDGAAADVWSCGVI.FVLMAGYLPFDEPN | 223 | + | 66.9 |
The name of the sequence with the match appears on the left; the start and end coordinates of the match appear on either side of the matching sequence; the match score appears on the right. The plus sign indicates the strand of the match (only meaningful when considering both strands of nucleotide sequences with the -2 option). The stars indicate the key positions of the motif: the alignment of the match to the key positions is shown. (The HTML format output does not include the stars over the matched sequence.)
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| Basic Options | |||
| -t | Output in text format only to standard output. | The program behaves as if -O glam2scan_out had
been specified. |
|
| -n | n | Report n matches. If scores are tied, they are sorted in alphabetical order of sequence name. If sequence names are also identical, the order is arbitrary. | |
| -2 | Search both strands of nucleotide sequences. | ||
| Advanced Options | |||
| The remaining options are somewhat specialized. For typical usage, it is reasonable to set them to exactly the same values as were used with glam2 to discover the motif. | |||
| -D | pseudocount | Specify the deletion pseudocount. | |
| -E | pseudocount | Specify the 'no-deletion' pseudocount. | |
| -I | pseudocount | Specify the insertion pseudocount. | |
| -J | pseudocount | Specify the 'no-insertion' pseudocount. | |
| -d | file | Specify a Dirichlet mixture file. | |
| -version | Display the version and exit. | Run as normal. | |
Some users may wish to make 'fake' glam2 motifs for input to glam2scan, for instance based on motifs found by other tools. Most of the glam2 output is ignored by glam2scan, and a minimal motif file looks like this:
**..****
seq1 10 HP..D.IG
seq2 5 HPGADLIG
seq3 7 HP..ELIG
seq4 5 HP..ELLA
The sequence names and coordinates are ignored, but some placeholder characters should be present. The stars indicating key positions are necessary, and the first and last columns must be starred.