General Information
| Description | A profile HMM to identify genes and bypass troublesome gene models in draft genomes |
| Homepage | https://github.com/dave-the-scientist |
Publications
Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes
Motivation:
Gene models from draft genome assemblies of metazoan species are often incorrect, missing exons or entire genes, particularly for large gene families. Consequently, labour-intensive manual curation is often necessary. We present Figmop (Finding Genes using Motif Patterns) to help with the manual curation of gene families in draft genome assemblies. The program uses a pattern of short sequence motifs to identify putative genes directly from the genome sequence. Using a large gene family as a test case, Figmop was found to be more sensitive and specific than a BLAST-based approach. The visualization used allows the validation of potential genes to be carried out quickly and easily, saving hours if not days from an analysis.
Availability and implementation:
Source code of Figmop is freely available for download at https://github.com/dave-the-scientist , implemented in C and Python and is supported on Linux, Unix and MacOSX.
Contact:
curran.dave.m@gmail.com
Supplementary information:
Supplementary data are available at Bioinformatics online.
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