The MG-RAST team is happy to acknowledge the use of the following great software and data products:

Databases

MG-RAST uses a number of databases integrated into the M5NR non-redundant database using the M5NR tools.

Protein databases:

• The SEED (Overbeek et al., NAR, 2005, Vol. 33, Issue 17)
• GenBank (Benson et al., NAR, 2011, Vol. 39, Database issue)
• RefSeq (Pruitt et al., NAR, 2009, Vol. 37, Database issue)
• IMG/M (Markowitz et al., NAR, 2008, Vol. 36, Database issue)
• UniProt (Apweiler et al., NAR, 2011, Vol. 39, Database issue)
• eggNOGG (Muller et al., NAR, 2010, Vol. 38, Database issue)
• KEGG (Kanehisa et al., NAR, 2008, Vol. 36, Database issue)
• PATRIC (Gillespie et al., Infect. Immun., 2011, Vol. 79, no. 11)

Ribosomal RNA databases:

• greengenes (DeSantis et al., Appl Environ Microbiol., 2006, Vol. 72, no. 7)
• SILVA (Pruesse et al., NAR, 2007, Vol. 35, issue 21)
• RDP (Cole et al., NAR, 2009, Vol. 37, Database issue)

Software

Bioinformatics codes:

• FragGeneScan (Rho et al, NAR, 2010, Vol. 38, issue 20)
• BLAT (J. Kent, Genome Res, 2002, Vol. 12, No. 4)
• QIIME (Caporaso et al, Nature Methods, 2010, Vol. 7, No. 5) (we also use the uclust that is part of QIIME)
• Biopython
• Bowtie (Langmead et al., Genome Biol. 2009, Vol 10, issue 3
• sff_extract, Jose Blanca & Joaquin Cañizares
• Dynamic Trim, part of SolexaQA, (Cox et al., (BMC Bioinformatics, 2011, Vol. 11, 485)
• FastqJoin

Web/UI tools:

• Krona (Ondov et. al. BMC Bioinformatics, 2011, Vol. 12, 385)
• Raphaël JavaScript Library (Dmitry Baranovskiy)
• jQuery
• Circos (Krzywinski et al., Genome Res. 2009, Vol. 19)
• cURL

Behind the scenes:

• Perl
• Python
• R
• Google’s V8  JavaScript engine
• Node.js
• JumpLoader Java file upload applet
• nginx
• OpenStack