Sample session:
helix% motifs -check
Motifs looks for sequence motifs by searching through proteins for the
patterns defined in the PROSITE Dictionary of Protein Sites and
Patterns. Motifs can display an abstract of the current literature on
each of the motifs it finds.
Minimal Syntax: % motifs [-INfile=]SW:Kad1_Human -Default
Prompted Parameters:
[-OUTfile=]kad1_human.motifs the output file name
Local Data Files:
-DATa=prosite.patterns file of protein sequence patterns
Optional Parameters:
-NOREFerence suppresses the PROSITE abstract for each pattern found
-FREquent shows motifs that are frequently found in proteins
-MISmatch=1 allows one mismatch
-NAMes writes output file in file-of-sequence-names format
-APPend appends the pattern data file to your output file
-SHOw shows every file searched, even if no pattern was found
-ONCe limits finds to patterns found only once
-MINCuts=2 limits finds to patterns found a minimum of 2 times
-MAXCuts=3 limits finds to patterns found a maximum of 3 times
-EXCLude=n1,n2 excludes patterns found between positions n1 and n2
-NOMONitor suppresses the screen trace showing each file
-NOSUMmary suppresses the screen summary at the end of the program
Add what to the command line ? -frequent
MOTIFs from what protein sequence(s) ? cram_craab.swissprot
What should I call the output file (* cram_craab.motifs *) ?
cram_craab.swissprot len: 46 ............................
Total finds: 2
Total length: 46
Total sequences: 1
CPU time (sec): 01.19
Output file: "/u5/susanc/cram_craab.motifs"
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