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The aim of the current project is to identify conserved functional elements from the mammalian genomes. Identification of evolutionarily conserved sequences helps to find a range of important functional elements that are otherwise difficult to detect, for example small RNA genes, promoters, transcription factor binding sites and other regulatory regions. For correct and efficient identification of conserved sequences we plan to test, compare and improve existing computational methods. The detection of conserved elements in studied genomes will be executed in three stages: alignment of syntenic genome regions, determination of evolutionarily conserved sequences and identification of functional sequence elements. The main emphasis is initially put into development of improved automatic methods for alignment of syntenic sequence regions, using orthologous genes as "anchors". The conserved sequences identified within this project will be entered into dedicated database and visualized with help of the UCSC genome browser. All methods are initially tested in 3-4 well-studied genomic regions where experimental data is available as a set of positive controls. After verification the methods will be applied to the whole genome sequences.
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