Pattern Recognition in Bioinformatics

The tetratricopeptide repeats (TPR)-like superfamily of proteins in Leishmania spp., as revealed by multi-relational data mining

“…A PPR motif is a degenerate 35-residue sequence, closely related to the 34-residue TPR motif. As reported in our earlier studies (Pacheco et al, 2007;Girão et al, 2008;Pacheco et al, 2009), we systematically solved inconsistencies in the motif annotation by manual expertise. Since motif occurrences are adjacent in sequences, we could define the motif sequence of a protein as the succession of motifs read from the N toward the C terminus.…”

“…In a first validation step we used the feature of trained HMMs to emit domain-specific sequences according to their model parameters. Sequences were compared with generated state paths in the same way as described earlier (Girão et al, 2008;Pacheco et al, 2009). The process of generation was repeated 10 times for every TPR-like motif.…”

“…As detailed previously (Girão et al, 2008), we have used the consensus sequence for TPR-like motif as a regular expression (1) to fully exploit the TPR motif finding problem in Leishmania spp. genomes.…”

“…In this paper, we present and discuss results regarding motif discovery methods, focusing in particular on our recent work in analyzing the tetratricopeptide repeat (TPR)-like superfamily of proteins in Leishmania spp. (Girão et al, 2008).…”

“…(Girão et al, 2008). We have, then, built a panel of the TPR-like superfamily of proteins, whose members can be further assigned functional roles for their containing motifs.…”