MSPcrunch
2.4a
a BLAST post-processing filter
Sonnhammer, Durbin
mspcrunch
mspcrunch
perl
"MSPcrunch"
0
blast_output
BLAST output File
perl
" $value"
2
blast_output
perl
1
output_options
Output Options
1
outfile
Result file
perl
" > $value "
mspcrunch.txt
1000
gapped
Make gapped alignment of ungapped-MSP contigs (-G)
perl
($value) ? " -G" : ""
1
big_pict
Big Picture (-P)
perl
($value) ? " -P" : ""
1
sfs
Produce SFS output (-H)
perl
($value) ? " -H" : ""
1
seqbl
Produce seqbl output (for Blixem) (-q)
perl
($value) ? " -q" : ""
1
ace
Produce .ace output (for ACEDB 4) (-4)
perl
($value) ? " -4" : ""
1
exblx
Produce exblx output (for easy parsing) (-x)
perl
($value) ? " -x" : ""
1
exbldb
Produce exbldb output (as exblx with query names) (-d)
perl
($value) ? " -d" : ""
1
fasta
Produce fasta output (unaligned, for mult.alignm.) (-2)
perl
($value) ? " -2" : ""
1
three_frame
Print 3 frame translation (blastn only) (-3)
perl
($value) ? " -3" : ""
1
footer
Print footer with parameters and stats (-f)
perl
($value) ? " -f" : ""
1
matches_one_line
For -P output, force all matches to the same subject on one line (-F)
perl
($value) ? " -F" : ""
1
perl
$big_pict
percentage_id
Print percentage identity (seqbl output only) (-i)
perl
($value) ? " -i" : ""
1
perl
$seqbl
stats_file
Output coverage stats to file (-o)
perl
($value) ? " -o $value" : ""
1
domainer
Produce output for Domainer (trim overlaps) (-D)
perl
($value) ? " -D" : ""
1
silent_mutations
Do Statistics of Silent mutations (only cDNA!) (-S)
perl
($value) ? " -S" : ""
1
all_expected
Print all Expected scores (default only when positive) (-X)
perl
($value) ? " -X" : ""
1
matrix_stats
Print statistics on used matrices (-E)
perl
($value) ? " -E" : ""
1
stats_without_X
Recalculate percentage identity, ignoring X residues. (-j)
perl
($value) ? " -j" : ""
1
ignore_hits
Ignore hits to earlier seqnames (for All-vs-All). (-A)
perl
($value) ? " -A" : ""
1
line_length
Line length of Wrapped alignment (0 -> no wrapping) (-W)
perl
(defined $value) ? " -W $value" : ""
1
wublast_numbered
indicate query insertions with numbers (For seqbl output from Wublast) (-N)
perl
($value) ? " -N" : ""
1
control_options
Control Options
1
dont_reject
Don't reject any MSPs (-w)
perl
($value) ? " -w" : ""
1
report_rejected
Report only rejected MSPs (-r)
perl
($value) ? " -r" : ""
1
threshold
Reject all matches with less than this % identity (-I)
perl
(defined $value) ? " -I $value" : ""
1
expect
Reject all matches with E-value higher than this value (-e)
perl
(defined $value) ? " -e $value" : ""
1
whole_contig
Coverage limitation requires whole contig to be covered (always for Blastp) (-a)
perl
($value) ? " -a" : ""
1
hits_to_self
Accept hits to self (-s)
perl
($value) ? " -s" : ""
1
no_hits_to_earlier
Ignore hits to earlier seqnames (for All-vs-All) (-A)
perl
($value) ? " -A" : ""
1
dont_mirror
Don't mirror (i.e. print the subject object) in ACE4 format (-M)
perl
($value) ? " -M" : ""
1
perl
$ace
old_cutoff
Use old step cutoffs for adjacency instead of the new continuous system. (-O)
perl
($value) ? " -O" : ""
1
input_options
Input Options
1
force_blastp
Force Blastp mode (default Blastx) (-p)
perl
($value) ? " -p" : ""
1
force_blastn
Force Blastn mode (default Blastx) (-n)
perl
($value) ? " -n" : ""
1
matrix
Scoring matrix (PAM or BLOSUM, see help) (-m)
perl
($value)?" -m /local/gensoft/lib/MSPcrunch/matrix/$value":""
1
You can give the name of:
. a PAM matrix : PAMxxx, where xxx ranges from 10 to 500, with a step of 10
. a BLOSUM matrix : BLOSUMxxx, where xxx ranges from 30 to 100, with a step of 5 - with the exception of BLOSUM62 which is the default scoring matrix
Several PAM (point accepted mutations per 100 residues) amino acid scoring matrices are provided in the BLAST software distribution, including the PAM40, PAM120, and PAM250. While the BLOSUM62 matrix is a good general purpose scoring matrix and is the default matrix used by the BLAST programs, if one is restricted to using only PAM scoring matrices, then the PAM120 is recommended for general protein similarity searches (Altschul, 1991). The pam(1) program can be used to produce PAM matrices of any desired iteration from 2 to 511. Each matrix is most sensitive at finding similarities at its particular PAM distance. For more thorough searches, particularly when the mutational distance between potential homologs is unknown and the significance of their similarity may be only marginal, Altschul (1991, 1992) recommends performing at least three searches, one each with the PAM40, PAM120 and PAM250 matrices.
query
Read in query seq (for rereading .seqbl files) (-Q)
perl
($value)? " -Q $query" : ""
1
8