Computational Biology
@ Comenius University in Bratislava

Juraj Mešťánek. Software for Annotation of Protein Coding Genes in Yeast Mitochondrial Genomes. Master thesis, Comenius University in Bratislava, 2010. Supervised by Broňa Brejová.

Download preprint: 10mestanekth.pdf, 800Kb

Download from publisher: https://stella.uniba.sk/zkp-storage/ddp/dostupne/FM/2010/2010-FM-oxpwYR/

Related web page: http://compbio.fmph.uniba.sk/mtconrad

Bibliography entry: BibTeX

Abstract:

In this thesis we present a software tool for automated
computational prediction of protein coding genes in yeast
mitochondrial genomes. Our tool is based on conditional random
fields (CRFs). To produce an accurate annotation, our tool
combines information from several different sources. We use
Exonerate to align reference proteins extracted from model
organisms to the genome being annotated. We also use RNAWeasel to
predict the positions of introns based on their characteristic
structural motifs. Finally, we use multiple alignment of
mitochondrial genomic sequences from several yeast species to
look for evolutionary signatures typical for protein-coding
regions. These three sources of information as well as the
studied nucleotide sequence form a set of observations used in
our CRF model to predict positions of exons and introns. We have
tested our tool on genes from 33 mitochondrial
genomes. Currently, we predict 78% of genes and 70% of exons
perfectly. In future we plan to make our tool available and easy
to use for the life science community.