Skip to main content
Fig. 3 | BMC Genomics

Fig. 3

From: A-GAME: improving the assembly of pooled functional metagenomics sequence data

Fig. 3

Identification of candidate genes/protein a. A-GAME offers a collection of tools and utilities for the functional annotation of proteins that can be used in order to facilitate the identification of genes with enzymatic activity of interest. a Concise report of PFAM protein domain annotation. The report is presented as an html page in a fasta-like format. Protein sequences are associated to their PFAM domains and a brief description. Hyperlinks to PFAM are included in the report in order to facilitate the retrieval of more complete information. For datasets where contig clustering (FosBin) or Sanger end-tag data are available, annotation of each inferred cluster is reported in a dedicated html page. Users can navigate through individual reports using hyperlinks provided at the top of the main page. b. Keyword search of PFAM domain annotation. Candidate genes with enzymatic activities of interest can be retrieved by performing keyword search of PFAM domain annotation by using the dedicated utility in A-GAME. Protein matching user provided keywords are reported in a dedicated report. c. Characterization of candidate proteins. The Interpro suite can be used for more specific annotation of functional domains in user selected subsets of genes to generate pages containing graphical depictions with descriptions and web-links to corresponding databases. A-GAME allows users to perform similarity searches against a local database containing more than 2500 Refseq bacterial proteomes to identify homologs of reconstructed ORFs

Back to article page