Open AccessConsPred: a rule-based (re-)annotation framework for prokaryotic genomes
Author(s) -
Thomas Weinmaier,
Alexander Platzer,
J. Howard Frank,
Hans-Jörg Hellinger,
Patrick Tischler,
Thomas Rattei
Publication year - 2016
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btw393
Subject(s) - perl , annotation , computer science , java , software , gene annotation , pipeline (software) , genome project , process (computing) , coding (social sciences) , gene prediction , data mining , genome , mit license , cloud computing , information retrieval , artificial intelligence , programming language , gene , biology , biochemistry , statistics , mathematics , operating system
The rapidly growing number of available prokaryotic genome sequences requires fully automated and high-quality software solutions for their initial and re-annotation. Here we present ConsPred, a prokaryotic genome annotation framework that performs intrinsic gene predictions, homology searches, predictions of non-coding genes as well as CRISPR repeats and integrates all evidence into a consensus annotation. ConsPred achieves comprehensive, high-quality annotations based on rules and priorities, similar to decision-making in manual curation and avoids conflicting predictions. Parameters controlling the annotation process are configurable by the user. ConsPred has been used in the institutions of the authors for longer than 5 years and can easily be extended and adapted to specific needs.
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