ProGeRF specifications

Information


Unique identifier OMICS_15742
Name Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function
Interface Web user interface
Restrictions to use None
Input data Receives as input parameters (i) a (multi)FASTA file, (ii) minimum size of the repetitive pattern, (iii) the minimum and maximum sizes of the motif (word DNA or amino acids length or sliding window length), (iv) maximum amount of gaps accepted between each motif of a repeat, (v) percentage of maximum degeneration accepted for a motif, (vi) overlapping percentage, and (vii) run mode, that is, whether using a FASTA file of DNA or of amino acids.
Input format FASTA
Output data A file with tabular data, where the columns represent the following information in this order: sequence id, sequence length, minimal repeat, tract length, start position, end position, total number of gaps, repetitive motif, statistic (only nucleotide), repeat sequence.
Output format TSV
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_15742
Name Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Genome and proteome sequences.
Input format FASTA
Output data A file with tabular data, where the columns represent the following information in this order: sequence id, sequence length, minimal repeat, tract length, start position, end position, total number of gaps, repetitive motif, statistic (only nucleotide), repeat sequence.
Output format TSV
Operating system Unix/Linux
Programming languages Perl
Parallelization OpenMP
Computer skills Advanced
Stability Stable
Source code URL http://64.79.105.19/ligp/?pg=manual#download
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


This tool is not available anymore.

ProGeRF article

ProGeRF funding source(s)
This work was supported by Coordenacao de Aperfeic¸ oamento de Pessoal de Nivel Superior (CAPES) [23038008852], FAPEMIG, and CNPq.

ProGeRF reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ProGeRF

Related Tools