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])]