MulPSSM

[…] kinase catalytic domain containing gene products using the HMMer method by querying each of the kinase domain containing proteins against the protein family HMMs available in the Pfam database [] and MULPSSM profiles [, ] of families in Pfam database. Transmembrane segments were detected using TMHMM []. […]

[…] %) [] than simple sequence profile search methods such as PSI-BLAST and HMMER2.0 (sensitivity around 20% at superfamily level) []. Some of the recent developments using the PSI-BLAST programs such as MulPSSM [] and Cascade BLAST [] have increased sensitivity of PSI-BLAST methods by a few percentage points, but they may not be suited for homology based structural modeling since they depend on PSI-B […]

[…] ous protein kinase subfamilies proposed by Hanks and Hunter classification scheme. RPS-BLAST has been used to search each of the putative protein kinases as a query against the database containing 55 Multiple Position Specific Scoring Matrices (MulPSSMs) created for the various subgroups of protein kinases in each of the subfamilies. Criteria used in identifying kinase subfamilies involved use of […]

[…] omain of these PKLNKs has been carried out using HMMer search methods by querying each of the PKLNK against the 10340 protein families HMMs available in the Pfam database (http://pfam.sanger.ac.uk/). MulPSSM (Multiple PSSM) [] approach was used further to assign domain to the region which has not been assigned using HMMer approach. Trans-membrane regions were detected using TMHMM []. […]

[…] Protein kinases are identified using a combination of profile-based search methods such as PSI-BLAST [] and RPS-BLAST [] using multiple profiles (MulPSSM) [,]. MulPSSM approach has been previously benchmarked and has been used in our previous kinome analysis for several other genomes [,,,,]. Summary of the main steps involved in the current ana […]