The purpose of this project is to utilize genomic data, primarily those concerned with sequences of complete intergenic regions of genomes, in order to learn more about functions of non-coding eukaryotic DNA. For this purpose, we developed a software tool OWEN for rapid, hierarchical alignment of very long sequences such that similarity between them can be represented by a chain of successive local alignments. Alignments obtained in this way were used for the following studies: - quantitative description of selective constraint revealed by Homo - Mus and Caenorhabditis elegans - C. briggsae alignments, analysis of domestication of ancient transposons MIR and L2 in mammals, and the classification of highly conserved, common fragments in mammalian non-coding DNA.
| Yampolsky, Lev Y; Allen, Chenoa; Shabalina, Svetlana A et al. (2005) Persistence time of loss-of-function mutations at nonessential loci affecting eye color in Drosophila melanogaster. Genetics 171:2133-8 |
| Jordan, I King; Kondrashov, Fyodor A; Adzhubei, Ivan A et al. (2005) A universal trend of amino acid gain and loss in protein evolution. Nature 433:633-8 |
| Yampolsky, Lev Y; Kondrashov, Fyodor A; Kondrashov, Alexey S (2005) Distribution of the strength of selection against amino acid replacements in human proteins. Hum Mol Genet 14:3191-201 |
| Kolker, Eugene; Makarova, Kira S; Shabalina, Svetlana et al. (2004) Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res 32:2353-61 |
| Kondrashov, Alexey S; Rogozin, Igor B (2004) Context of deletions and insertions in human coding sequences. Hum Mutat 23:177-85 |
| Arnegard, Matthew E; Kondrashov, Alexey S (2004) Sympatric speciation by sexual selection alone is unlikely. Evolution Int J Org Evolution 58:222-37 |
| Bazykin, Georgii A; Kondrashov, Fyodor A; Ogurtsov, Aleksey Y et al. (2004) Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature 429:558-62 |
| Matveeva, Olga V; Foley, Brian T; Nemtsov, Vladimir A et al. (2004) Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. BMC Bioinformatics 5:44 |
| Shabalina, Svetlana A; Ogurtsov, Aleksey Y; Rogozin, Igor B et al. (2004) Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. Nucleic Acids Res 32:1774-82 |
| Kondrashov, Fyodor A; Ogurtsov, Aleksey Y; Kondrashov, Alexey S (2004) Bioinformatical assay of human gene morbidity. Nucleic Acids Res 32:1731-7 |
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