Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes

Motivation: The sheer scale of the metagenomic and metatranscriptomic datasets that are now available warrants the development of automated protocols for organizing, annotating and comparing the samples in terms of their metabolic profiles. We describe a user-friendly java program FROMP (Fragment Recruitment on Metabolic Pathways) for mapping and visualizing enzyme annotations onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways or custom-made pathways and comparing the samples in terms of their Pathway Completeness Scores, their relative Activity Scores or enzyme enrichment odds ratios. This program along with our fully configurable PERL-based annotation organization pipeline Meta2Pro (METAbolic PROfiling of META-omic data) offers a quick and accurate standalone solution for metabolic profiling of environmental samples or cultures from different treatments. Apart from pictorial comparisons, FROMP can also generate score matrices for multiple meta-omics samples, which can be used directly by other statistical programs. Availability: The source code and documentation for FROMP can be downloaded from https://sites.google.com/site/dhwanidesai/home/software along with the Meta2Pro collection of PERL scripts. Supplementary data are available at https://sites.google.com/site/dhwanidesai/home/fromp_suppl. Contact: Dhwani.Desai@Dal.Ca Supplementary information: Supplementary data are available at Bioinformatics online.