ProteinDigester

This application digests fasta proteins and return peptide digests (sequence, molecular weight and isoelectric point).

usage: ProteinDigester <Fasta> [-a] [-d <arg>] [-e <arg>] [-f <arg>] [-h]
       [-i <arg>] [-l <arg>] [-m <arg>] [-o <arg>] [-p <arg>] [-q] [-v]
 -a,--average                     set the average mass accuracy for
                                  peptide mass calculation
                                  by default: monoisotopic.
 -d,--delimiter <arg>             define the field delimiter to display
                                  by default: \t.
 -e,--enzymes <arg>               define enzymes that digest proteins
                                  separately with:
                                  enzyme name among 'Caspase-1, Caspase-10, Glu-C_bicarbonate, Caspase-3,
                                  Thermolysine, Lys-C, Pepsin_pH1.3, Caspase-8, Glu-C_phosphate, Caspase-9,
                                  Caspase-5, CNBr, ChymoTrypsin_lowspec, Trypsin, ChymoTrypsin_FYL,
                                  Proteinase-K, Caspase-7, Pepsin_pHgt2, ChymoTrypsin_highspec,
                                  BNPS-Skatole, Enterokinase, Caspase-6, Arg-C, Asp-N, ChymoTrypsin_FYLW,
                                  Caspase-4, Caspase-2'.
                                  or custom motifs respecting the following grammar:
								  <pre-cut> <cut-token> <post-cut>
                                  <cut-token> := '|'
                                  <pre-cut> := (<AA> or <AA-class>)+
                                  <post-cut> := (<AA> or <AA-class>)+
                                  <AA> := [A-Z]
                                  <AA-class> := '[' AA+ ']'
                                  by default: Trypsin.
 -f,--fields <arg>                define the fields to display
                                  (1:Sequence, 2:MW, 3:pI, 4:Enz, 5:MC)
                                  by default: [1, 2, 3].
 -h,--help                        print this message.
 -i,--setting-file <arg>          give a property file with all input
                                  settings.
 -l,--length <arg>                define a filter over length of digested
                                  peptides
                                  by default: 5.
 -m,--max-missed-cleavage <arg>   define the number of maximum missed
                                  cleavages (for digestion)
                                  by default: 1.
 -o,--output <arg>                set the output filename
                                  
 -p,--precision <arg>             define the number of fractional digits
                                  for output
                                  by default: 6.
 -q,--quiet                       quiet mode (verbose off)
                                  by default: false.
 -v,--version                     print the version info.
      

# a first way to execute the application with lots of options
$ java -jar ProteinDigester.jar -a -e Lys-C -f 1,2,4,5 -l 6 -p4 -q -o /tmp/dig.tsv uniprot-human.fasta

# .. or the more compact way with all options defined in a setting file
$ java -jar ProteinDigester.jar -i settings.properties uniprot-human.fasta
      

The latest version is v1.22 - Download app.

Rel1.22

Rel1.2

Rel1.1