Allows users to model sequence evolution under domain constraints. Revolver utilizes pattern of sequence differences between homologous sequences for describing the constrained evolutionary process to which a protein domain is subjected. It can be used to perform simulations under domain constraints applicable to all proteins even if they show no significant sequence similarity to any of the domains for which public profile hidden Markov models (pHMMs) are available.
Determines novel multiciliogenesis genes. BLUR employs a fine-grained comparative genomic method to proceed. It is designed to deal with a whole proteome level. This tool identifies proteins that present an atypical pattern of conservation among different species resulting from divergence or loss of a domain and/or motif in a specific taxon. It enables the discovery of cases of abnormal divergence and differential conservation.
Aims to predict the light-absorption properties of microbial rhodopsin proteins. GrplassoSeq is a statistical model describing the relationship between amino-acid sequences and absorption wavelengths. Moreover, this tool demonstrates its utility for understanding colour tuning rules and predicting absorption wavelengths.
Infers high confidence associations between enzyme commission (EC) numbers and Pfam domains. EC-PSI is designed to directly find associations from existing EC-chain associations from SIFTS and EC-sequence associations from SwissProt and TrEMBL. This algorithm collects and integrates a large number of existing EC-chain/sequence annotations, allowing it to deduce over 8000 direct EC-Pfam associations with respect to the manually curated InterPro database.
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