chainsaw

chainsaw is a command-line utility for in-silico digest of amino acid sequences. The utility reads a fasta file and outputs a tab-separated file with the following fields:

sequence : the amino acid sequence of the theoretical peptide
protein : the protein referenced in the fasta file
mass: mass of the theoretical peptide
missedCleavages: number of missed cleavages observed
specificity:

0 = nonspecific cleavage on both N and C termini
1 = nonspecific cleavage on one of the N or C termini
2 = specific cleavage on both termini

0 = nonspecific N terminus cleavage
1 = specific N terminus cleavage

0 = nonspecific C terminus cleavage
1 = specific C terminus cleavage

A variety of options are supported to customize the digest. In particular, one can specify a digestion enzyme in one of three ways:

(1) -e, --proteolyticEnzyme: use one of the enumerated proteolytic enzymes provided
(2) -d, --digestionMotif: use a digestion motif for the enzyme of choice (see example below)
(3) -r, --cleavageAgentRegex: use a regular expression to specify cleavage (see example below)

Additional options are shown in the usage string, reproduced below. To show this string on the command line, run chainsaw without any arguments. Usage: chainsaw [options] [filenames]

Options:
  -e [ --proteolyticEnzyme ] arg        : specify proteolytic enzyme for digest
                                       ion. Options: trypsin, chromotrypsin, cl
                                       ostripain, cyanogenBromide, pepsin. 
                                       Default : trypsin
  -d [ --digestionMotif ] arg           : specify a digestion motif (e.g. tryps
                                       in = "[KR]|[^P]")
  -r [ --cleavageAgentRegex ] arg       : specify a cleavage agent regex (e.g. 
                                       trypsin = "(?<=[KR])(?!P)")
  -n [ --numMissedCleavages ] arg (=0)  : specify number of missed cleavages to
                                       allow.
  -s [ --specificity ] arg              : specify minimum specificity. Options:
                                       non, semi, fully. 
                                       Default: fully
  -m [ --minLength ] arg (=0)           : specify minimum length of digested pe
                                       ptides
  -M [ --maxLength ] arg (=100000)      : specify maximum length of digested pe
                                       ptides
  -p [ --massPrecison ] arg (=12)       : specify precision of calculated mass 
                                       of digested peptides
  --benchmark                           : do not write results

Examples:

Download an example fasta file HERE

• chainsaw bsa_precursor.fa
  (digestion with default params)
• chainsaw -e cyanogenBromide bsa_precursor.fa
  (digestion with cyanogen bromide, all other params default)
• chainsaw -n 2 -s semi bsa_precursor.fa
  (digestion with trypsin, 2 missed cleavages, semi-specific cleavage)