---
name: "prok-geneseek"
section: "1"
platform: "linux"
package: "python3-biotools"
version: "1.2.12-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/prok-geneseek"
---

# prok-geneseek(1)

\<optional description of the program\>

## NAME

prok-geneseek - \<optional description of the program\>

## SYNOPSIS

**prok-geneseek** \[*options*\] *\<database\> \<sequences* ...*\>*

## OPTIONS

- **-h**, **--help**

  show this help message and exit

- **-S** START, **--start**=*START*

  define a start codon \[default: **-S** ATG\]

- **-E** STOP, **--stop**=*STOP*

  define a stop codon \[default: **-E** TAG **-E** TAA **-E** TGA\]

- **-j** THREADS, **--threads**=*THREADS*

  number of threads \[default: 16\]

- **-p** PROCESSES, **--processes**=*PROCESSES*

  number of parallel processes to run \[default: 2\]

- **-e** EVALUE, **--evalue**=*EVALUE*

  maximum e-value \[default: 1e-30\]

- **-I** IDENTITY, **--identity**=*IDENTITY*

  minimum percent identity \[default: 0.45\]

- **-L** FRACTION, **--length**=*FRACTION*

  allowable relative error in hit length \[default: 0.2\]

- **-O** bases, **--orflen**=*bases*

  minimum allowable length for ORFs \[default: 300\]

- **-d** DIRECTORY, **--directory**=*DIRECTORY*

  set working directory \[default: current\]

- **-P** PLOTTER, **--plotter**=*PLOTTER*

  plotting module \[default: biotools.analysis.plot\]

- **-v**, **--verbose**

  print debug messages \[default: False\]

- **--no-plots**

  suppress the drawing of plots \[default: False\]

- **--no-predict**

  don't predict genes, instead treat the input files as predicted genes \[default: False\]

- **--no-cluster**

  don't cluster the sequences, instead treat the input files as alignments \[default: False\]

- **--no-rename**

  don't rename the fasta and clustal files \[default: False\]

- **--no-reports**

  don't generate files for variance data \[default: False\]

- **--no-calculation**

  don't calculate sequence variance \[default: False\]

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.