Gene family identification network design

The exponential accumulation of molecular data will facilitate the discovery of new knowledge by using information embedded within families of homologous sequences. As an approach to the management and analysis of sequence data, we have developed an integrated system, termed GeneFIND (Gene Family Identification Network Design), for database searching against gene families. It provides rapid and accurate protein family identification by combining global and motif sequence similarities and incorporating ProClass family information. Multilevel filters are used, starting with the MOTIFIND neural network and BLAST search, followed by SSEARCH alignment motif pattern match, hidden Markov modeling of motifs and ClustalW motif alignment. GeneFIND has been implemented as a full-scale system for the classification of more than 1000 ProSite and 3000 PIR families. It is used to identify thousands of new family members and is well suited for genomic sequence analysis.