I was catching up on reading past BioMed Central Article Alert emails & I saw a resource that I wanted to pass on to you. The resource is WebCARMA, and is a web version of the CARMA analysis program (not too hard to guess that, though huh?!?). Yea, but what is CARMA (the software version with a “C” rather than the philosophical one with a “K”)? According to Krause et al., 2008 CARMA is:
The algorithm searches for conserved Pfam domain and protein families in the unassembled reads of a sample. These gene fragments (environmental gene tags, EGTs), are classified into a higher-order taxonomy based on the reconstruction of a phylogenetic tree of each matching Pfam family. The method exhibits high accuracy for a wide range of taxonomic groups, and EGTs as short as 27 amino acids can be phylogenetically classified up to the rank of genus.
To quote Gerlach et al., 2009 WebCARMA is:
WebCARMA, a refined version of CARMA available as a web application for the taxonomic and functional classification of unassembled (ultra-)short reads from metagenomic communities.
I didn’t actually run WebCARMA because, well, I don’t actually have a metagenome in my back pocket (but later I might just sneak over to IMG/M & download some FASTA metagenomic sequence so I can play…). I did read the documentation & it sounds pretty neat. CARMA doesn’t actually create taxonomic profiles, but it does create taxonomic assignments for your short metagenome reads, outputs lots of output files full of information, and provides some perl scripts for creating the taxonomic profiles. You can read about what WebCARMA does here, and download example output files here.
You do need to email for a login URL, and there are limits to how much you can analyze online (100 megabytes within 4 weeks in total), but I’m not sure that I’ve seen a resource that does exactly what CARMA/WebCARMA does. If you use WebCARMA, could you let me know what you think of it? And if you use other similar software, what is it? Thanks!
W. Gerlach, S. Jünemann, F. Tille, A.Goesmann and J. Stoye
WebCARMA: A Web Application for the Functional and Taxonomic Classification of Unassembled Metagenomic Reads
BMC Bioinformatics 2009, 10:430
L. Krause, N.N. Diaz, A. Goesmann, F. Rohwer, S. Kelley, R.A. Edwards J. Stoye,
Phylogenetic Classification of Short Environmental DNA Fragments,
Nucleic Acids Research 2008 36(7):2230-2239; doi:10.1093/nar/gkn038.