Table 1.

BioRuby modules

Category	Module list
Object	Sequence, pathway, tree, bibliography reference
Sequence	Manipulation, translation, alignment, location, mapping, feature table, molecular weight, design siRNA, restriction enzyme
Format	GenBank, EMBL, UniProt, KEGG, PDB, MEDLINE, REBASE, FASTA, FASTQ, GFF, MSF, ABIF, SCF, GCG, Lasergene, GEO SOFT, Gene Ontology
Tool	BLAST, FASTA, EMBOSS, HMMER, InterProScan, GenScan, BLAT, Sim4, Spidey, MEME, ClustalW, MUSCLE, MAFFT, T-Coffee, ProbCons
Phylogeny	PHYLIP, PAML, phyloXML, NEXUS, Newick
Web service	NCBI, EBI, DDBJ, KEGG, TogoWS, PSORT, TargetP, PTS1, SOSUI, TMHMM
OBDA	BioSQL, BioFetch, indexed flat files

Refer to www.bioruby.org for an explanation of all acronyms.