Computational methods of gene finding as well as gene and protein sequence analysis are being used to study the structure, function and evolution of proteins and non-coding RNAs (ncRNAs). We have developed methods to effectively identify ncRNAs in genomic sequences and have applied these methods on a large number of ncRNA families, including SRP RNA and RNase P/MRP RNA. We have identified a large number of previously unrecognized homologues and these results have allowed a better understanding of the secondary structure and evolution of these RNAs. The evolution of proteins have/are been studied in a number of projects where we make use of tools such as gene prediction, profile-based searches and methods of phylogenetic analysis. Examples include 1) protein subunits of SRP and RNase P, 2) the bacterial translocation factor YidC, 3) the mitochondrial transcription termination factor MTERF, and 4) protein subunits of the mediator of transcriptional control. Finally, mucins, heavily glycosylated proteins that cover and protect epithelial cell surfaces, are being studied through a bioinformatic inventory of these proteins in a number of animals.
Rosenblad MA, Davila ML., Piccinelli P and Samuelsson T. (2006) Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes. Nucl Acids Res, In press
Lang T, Hansson GC and Samuelsson T. (2006) An inventory of mucin genes in the chicken genome shows that the mucin domain of Muc13 is encoded by multiple exons and that ovomucin is part of a locus of related gel-forming mucins. BMC Genomics. 7:197
Piccinelli P, Rosenblad MA and Samuelsson T. (2005) Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res. 33:4485-95.
Lang T, Alexandersson M, Hansson G and Samuelsson T. (2004) Bioinformatic identification of polymerizing and transmembrane mucins in the puffer fish Fugu rubripes. Glycobiology 14:521-527.
Alm Rosenblad M, Zwieb C, and Samuelsson T. (2004) Identification and comparative analysis of components from the signal recognition particle in protozoa and fungi. BMC Genomics. 5:5