umgap prot2tryp
Splits a FASTA stream into tryptic peptides.
The umgap prot2tryp
command takes one or more amino acid sequences as input and applies an in
silico peptide digest.
Usage
The input is given in a FASTA format on standard input with a single peptide per FASTA header, which may be hardwrapped with newlines. The peptides resulting from the digest are written in FASTA format to standard output, with multiple peptides per FASTA header, separated by newlines.
$ cat input.fa >header1 AYKKAGVSGHVWQSDGITNCLLRGLTRVKEAVANRDSGNGYINKVYYWTVDKRATTRDALDAGVDGIMTNYPDVITDVLN $ umgap prot2tryp tryptic-lca.index < input.fa >header1 AYK K AGVSGHVWQSDGITNCLLR GLTR VK EAVANR DSGNGYINK VYYWTVDK R ATTR DALDAGVDGIMTNYPDVITDVLN
Using the -p flag, you can change the splitting pattern. The default pattern ([KR])([^P])
splits between any Lysine (K) or Arginine (R), followed by any amino acid that is not Proline
(P).
- -h / --help
- Prints help information
- -V / --version
- Prints version information
- -p / --pattern p
- The cleavage-pattern (regex), i.e. the pattern after which the next peptide will be cleaved for tryptic peptides) [default:
([KR])([^P])
]