Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes

Abstract

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

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

“…We downloaded genome data either from NCBI servers or the genome project websites. We then used the F igmop [ 55 ] pipeline to find contigs and scaffolds in the genomes with NLR-B30.2 candidates on them. The F igmop pipeline builds a profile of conserved motifs from a starting set of sequences and uses these to search a target database with the MEME software suite [ 56 ].…”

Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes

“…Panagrolaimus species, but present in the amphimictic representatives and in other tylenchines. To explore and independently validate this pattern of absence, we used figmop (Curran et al 2014) to build a gene model based on motifs in the C. elegans gene and screened the P. sp. PS1159 genome.…”

“…OrthoFinder based on Diamond (Buchfink et al 2014) BLAST was only used in the GRAMPA (Thomas et al 2016) analysis, since the output contains gene trees for each cluster (see section on ploidy below). In cases were OrthoMCL and OrthoInspector grossly disagreed or the presence/absence pattern across species appeared inconsistent in the GRN analysis, we directly screened genomes for the presence of a gene using the HMM profile figmop pipeline (Curran et al 2014).…”

Genome Informatics 2016

“…Sonja Dunemann (University of Calgary, Canada) described the caution necessary before claiming horizontal gene transfer. David Curran (University of Calgary, Canada) presented work on Figmop [13], a profile hidden Markov model that identifies orthologs not identifiable using the popular Basic Local Alignment Search Tool (BLAST) method.…”