BMC Genomics 2009, 10:622 http://www.biomedcentral.com/1471-2164/10/622 almost all of them having known cDNA data available and many of them known to get expressed in various tis- sue or cell types. Our current survey enabled us to recog- nize many important kinase splice variants which might be involved in diverse signal transduction pathways and have different modes of regulation. List of newly recog- nized human kinase splice variants includes several exam- ples which are not yet studied experimentally. Future direction could aim at studying sub-cellular localization of the kinase splice variants in the types of cells, their role in biological processes, modes of regulation and substrate specificity which will give insight into the human signal transduction pathway. Methods The complete set of predicted protein sequences from the ORFs of the human genome has been obtained from ENSEMBL [release 52] http://www.ensembl.org. We have surveyed the genome, for Ser/Thr and Tyr protein kinases using sensitive sequence profile matching algorithms. The sequence search tools and other strategies for domain identification and sub-family classification used in this study by employing PSI-BLAST [38], Reverse PSI - BLAST (RPS-BLAST) [39], HMMer [40] which match Hidden Markov Models (HMMs) to identify protein kinase cata- lytic domain and their co-occurring domains. Search pro- cedures such as PSI-BLAST and RPS-BLAST have been used at stringent E-value cut off of 0.0001. Searches performed using HMMer with an E-value cut-off of 0.01 or below have been shown to nearly eliminate any spurious hits. Hits lacking significant sequence similarity with the query have been further examined, manually. The final data set of predicted putative human protein kinases has been obtained from the compilation of hits obtained using var- ious procedures. The program CD-HIT [41] was used in order to eliminate redundant sequences. The sequence identity shared between any two putative protein kinase sequences in the data set is less than 100%, suggesting that the data set is devoid of redundant sequences. Multiple sequence alignment of the kinase catalytic domains of the putative human protein kinases has been carried out using ClustalW [42]. Information on cell/tissue types where various kinases are expressed has been retrieved from ENSEMBL http://www.ensembl.org and it has been observed that 498 protein kinases are getting expressed in various tissue types (Additional file 3). Classification of human protein kinases into subfamilies Protein kinases discussed in the current analysis have been classified into various 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 identi- fying kinase subfamilies involved use of stringent condi- tions such as alignment coverage of the sequence greater than 70% over the kinase domain region and sequence identity cut-off of 30% aside from satisfying the stringent e-value cutoff criteria. Domain assignment to the non-catalytic regions of the kinase containing genes has been carried out using the HMM search methods by querying each of the kinase domain containing sequences against the 9318 protein family HMMs available in the Pfam database release 23 [43]. Information on splice variants for these putative protein kinases was taken from BioMart data mining tool availa- ble in ENSEMBL database which has entry for genes, their transcripts and protein products. In ENSEMBL, an initial alignment of mRNA and protein is performed against the genome. All overlapping transcripts are clustered under one gene name and deemed 'splice variants'. So the gene products pointing to a single gene are defined as splice variants by ENSEMBL http://www.ensembl.org. Authors' contributions KA carried out the analysis. NG has developed the web- site. KA and NS have drafted the manuscript. All authors read and approved the final manuscript. Additional material Additional file 1 List of all the 918 human protein kinases. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-622-S1.DOC] Additional file 2 List of human protein kinase splice variants with different domain organisations. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-622-S2.DOC] Additional file 3 List of human kinase splice variants with information on their expres- sion in various tissue/cell types obtained from ENSEMBL database. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-622-S3.XLS] Acknowledgements This research is supported by the Department of Biotechnology, Govern- ment of India to NS. NG is supported by the Indian Institute of Science Centenary Postdoctoral Fellowship. Page 5 of 7 (page number not for citation purposes)