MOTIF (GenomeNet, Japan) - I recommend this for the protein analysis, I have tried phage genomes against the DNA motif database without success.
Amino acid sequence analysis manual#
InterPro 5 - includes PROSITE, HAMAP (High-quality Automated and Manual Annotation of Proteins), Pfam (protein Families), PRINTS, ProDom, SMART (a Simple Modular Architecture Research Tool), TIGRFAMs, PIRSF (Protein Information Resource), SUPERFAMILY, CATH-Gene3D (Class, Architecture, Topology, Homologous superfamily), and PANTHER (Protein ANalysis THrough Evolutionary Relationships) classification systems. ( Reference: Jones, P. Motif Scan – (MyHits, SIB, Switzerland) includes Prosite, Pfam and HAMAP profiles. Several great sites including the first four which are meta sites: Alternatively, use a meta site such as MOTIF (GenomeNet, Institute for Chemical Research, Kyoto University, Japan) to simultaneously carry out Prosite, Blocks, ProDom, Prints and Pfam search I recommend that you check your protein sequence with at least two different search engines. For background information on this see PROSITE at ExPASy. Online Analysis Tools - Motifs MOTIFS : USING DATABASES & CREATING YOUR OWNīACKGROUND INFORMATION: Proteins having related functions may not show overall high homology yet may contain sequences of amino acid residues that are highly conserved.