Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models.
- Includes a suite of tools used for querying sequences, search terms, accessions against their databases; useful for additional motif/domain identification analysis
- HMMER3 tool to build HMM profiles from multiple alignments
- Many pattern finding tools
Requires some knowledge of the programs used for sequence analysis, alignment, matching, etc.
- Pagni, M., Ioannidis, V., Cerutti, L., Zahn-Zabal, M., Jongeneel, C. V., & Falquet, L. (2004). MyHits: a new interactive resource for protein annotation and domain identification. Nucleic acids research, 32(suppl_2), W332-W335.
- Pagni, M., Ioannidis, V., Cerutti, L., Zahn-Zabal, M., Jongeneel, C. V., Hau, J., ... & Falquet, L. (2007). MyHits: improvements to an interactive resource for analyzing protein sequences. Nucleic acids research, 35(suppl_2), W433-W437.