ProGeRF specifications

Unique identifier:
OMICS_15742
Interface:
Web user interface
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.
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.
Computer skills:
Basic
Maintained:
Yes
Name:
Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function
Restrictions to use:
None
Input format:
FASTA
Output format:
TSV

ProGeRF specifications

Unique identifier:
OMICS_15742
Software type:
Application/Script
Restrictions to use:
None
Input format:
FASTA
Output format:
TSV
Programming languages:
Perl
Computer skills:
Advanced
Source code URL:
http://64.79.105.19/ligp/?pg=manual#download
Name:
Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function
Interface:
Command line interface
Input data:
Genome and proteome sequences.
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.
Operating system:
Unix/Linux
Parallelization:
OpenMP
Maintained:
Yes

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ProGeRF distribution

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ProGeRF support

Documentation

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Publications

Funding source(s)

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

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