Format

Send to

Choose Destination
Bioinformatics. 2015 Oct 15;31(20):3345-7. doi: 10.1093/bioinformatics/btv361. Epub 2015 Jun 15.

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

Author information

1
Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada.
2
Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC, Canada and.
3
Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada.
4
Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada, Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC, Canada and.

Abstract

Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database.

AVAILABILITY AND IMPLEMENTATION:

MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2.

CONTACT:

shallam@mail.ubc.ca

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26076725
PMCID:
PMC4595896
DOI:
10.1093/bioinformatics/btv361
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center