MetaQuery: A web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome

Bioinformatics

Volumn 31, Issue 20, 2015, Pages 3368-3370

  Nayfach, Stephen ^a   Fischbach, Michael A ^a   Pollard, Katherine S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENE; DIABETES MELLITUS; FECES; GENETICS; HUMAN; INFLAMMATORY BOWEL DISEASE; INTERNET; INTESTINE FLORA; METAGENOMICS; MICROBIOLOGY; MOLECULAR GENETICS; PROCEDURES; SOFTWARE;

DIABETES MELLITUS; FECES; GASTROINTESTINAL MICROBIOME; GENES, BACTERIAL; HUMANS; INFLAMMATORY BOWEL DISEASES; INTERNET; METAGENOMICS; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE;

EID: 84947772278     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv382     Document Type: Article

References (11)

1. Aagaard, K. et al. (2013). The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J, 27, 1012-1022.
2. Abubucker, S. et al. (2012). Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol., 8, e1002358.
3. Altschul, S.F. et al. (1990). Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
4. Donia, M.S. et al. (2014). A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell, 158, 1402-1414.
5. Li, J. et al. (2014). An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol., 32, 834-841.
6. Manor, O., Borenstein, E. (2015). MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. Genome Biol., 16, 53.
7. Nayfach, S., Pollard, K.S. (2015). Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol., 16, 51.
8. Schnoes, A.M. et al. (2009). Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol., 5, e1000605.
9. Segata, N. et al. (2012). Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods, 9, 811-814.
10. Sonnenburg, E.D. et al. (2010). Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell, 141, 1241-1252.
11. Zhao, Y. et al. (2012). RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics, 28, 125-126.