ziggypep

January 19, 2026 ยท View on GitHub

CI GitHub release License: GPL v3 Conda Language: Perl 5

ziggypep

Identify signal peptides in protein sequnces

Description

I want to make an free, unencumbered tool to identify signal peptides in protein sequences. The existing tools are either not open source, require an academic licence, only have a webserver, or not installable in Bioconda.

Ziggypep uses a very simplistic method which achieves 1026/1320 (72%) on a positive test set and 1234/1334 (93%) on a negative test set.

Installation

conda install -c bioconda -c conda-forge ziggypep

Quick start

% ziggypep test/test.faa.gz

WP_456262590.1  0
WP_407478045.1  14      MDTLQAIILAIVEG
WP_456262591.1  0
WP_456262592.1  38      MKQLPTITDSYKKEVQKSVLSIILFFTVYFILILFSLA
WP_249063066.1  0
WP_016200366.1  0
WP_078792968.1  20      MKKIAVLITMLMTGIIFAQV

# only list those with signal peptides
% ziggypep -s test/test.faa.gz

WP_407478045.1  14      MDTLQAIILAIVEG
WP_456262592.1  38      MKQLPTITDSYKKEVQKSVLSIILFFTVYFILILFSLA
WP_078792968.1  20      MKKIAVLITMLMTGIIFAQV

Usage

Input

You must provide protein FASTA files:

>WP_016198972.1 
MEQNITLVWENCLSFMRDNLNSIEEKEGVNKLDDSFDLL
LSLLSAALKKNIGKGVKLWYSVMENKPVGKIPPVTIQK
>WP_271151124.1
MVNIDSQLNAMLTFDNFIEGESNKFASTVARTIAKRPG
PDKVVLYVSSEKFIQQFVSAAKAQNKTDF
...

They can be compressed with .gz or .bz2. You can provide multiple files if you like.

% ziggypep test/test.ffa.gz test/pos.faa test/neg.faa.bz2

Output

Output is tab-separated 3 columnns with no header.

  • Column 1 = sequence name, from the > FASTA header
  • Column 2 = length of signal peptide, 0 if none
  • Column 3 = signal peptide sequence, empty if none
WP_407478045.1  14      MDTLQAIILAIVEG
WP_456262591.1  0
WP_456262592.1  38      MKQLPTITDSYKKEVQKSVLSIILFFTVYFILILFSLA
WP_249063066.1  0

Options

  -h       Print this help
  -v       Print version and exit
  -C       Show citation and exit
  -q       No output while running, only errors
  -s       Only print postive results

Etymology

This tool finds signal peptides. I like the name "Ziggy" - I have a family member with that name, I love David Bowie's Ziggy Stardust, Also, it rhymes with Iggy Pop who is also a rock legend who worked with Bowie in his early career. Ziggy was the "A.I" in the classic 1989 sci-fi series Quantum Leap.

References

Feedback

File questions, bugs, or ideas on the Issues page

License

GPLv3

Author

Torsten Seemann