ABFGP specifications

Information


Unique identifier OMICS_33298
Name ABFGP
Alternative name Alignment-Based Fungal Gene Prediction
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A list of orthologous gene loci.
Output data A file containing the predicted gene model and several features that assist manual inspection of the predicted gene model.
Output format GFF
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.f
Stability Stable
Maintained Yes

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Versioning


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Maintainers


  • person_outline Pierre de Wit
  • person_outline Ate van der Burgt

Publication for Alignment-Based Fungal Gene Prediction

ABFGP citation

library_books

Automated alignment based curation of gene models in filamentous fungi

2014
BMC Bioinformatics
PMCID: 3898260
PMID: 24433567
DOI: 10.1186/1471-2105-15-19

[…] the Joint Genome Institute (JGI) [] (Additional file ). Available unigenes from ten fungal species were downloaded from the JGI and The Gene Index Project (http://compbio.dfci.harvard.edu/tgi/). The ABFGP method uses several third party applications: BLAST 2.2.8, ClustalW 2.0.12, HMMER 2.3.2, SignalP 3.0, TMHMM 2.0, transeq, getorf and tcode from EMBOSS 6.2.0. […]

ABFGP institution(s)
Laboratory of Phytopathology, Wageningen University & Research Centre, Wageningen, The Netherlands; Applied Bioinformatics, Plant Research International, Wageningen University & Research Centre, Wageningen, The Netherlands; Laboratory of Genetics, Wageningen University & Research Centre, Wageningen, The Netherlands
ABFGP funding source(s)
Supported in part by the laboratory of Phytopathology of Wageningen University and a grant from The Royal Netherlands Academy of Arts and Sciences and in part by the Applied Bioinformatics Group of Wageningen University.

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