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

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 an...

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Published inBioinformatics Vol. 31; no. 20; pp. 3345 - 3347
Main Authors Konwar, Kishori M, Hanson, Niels W, Bhatia, Maya P, Kim, Dongjae, Wu, Shang-Ju, Hahn, Aria S, Morgan-Lang, Connor, Cheung, Hiu Kan, Hallam, Steven J
Format Journal Article
LanguageEnglish
Published England Oxford University Press 15.10.2015
Subjects
Algorithms
Annotations
Applications Notes
Applications programs
Bioinformatics
Computer programs
Databases, Genetic
Enzymes
Genomics - methods
High-Throughput Nucleotide Sequencing - methods
Humans
Information Storage and Retrieval
Molecular Sequence Annotation
Phylogeny
Searching
Sequence Analysis, DNA - methods
Software
Transformations
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Summary: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. MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2. shallam@mail.ubc.ca Supplementary data are available at Bioinformatics online.
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Associate Editor: Alfonso Valencia
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btv361