Phylogenetic Profiling
نویسندگان
چکیده
Phylogenetic profiling involves the study of the occurrence of gene families across fully sequenced genomes. For any gene, it is possible to create a phylogenetic profile which encodes the presence or absence of homologs of the gene across organisms. The comparison of phylogenetic profiles may be used to measure the evolutionary distance between organisms leading to the reconstruction of phylogenetic trees. The pair-wise comparison of phylogenetic profiles allows us to identify genes that co-occur across organism and are likely to participate within the same pathway or protein complex. Finally, by comparing phylogenetic profiles to phenotypic profiles that encode the presence or absence of phenotypes across organisms, it is possible to infer that a gene is partially responsible for establishing a phenotype. These techniques are currently used to survey about one hundred fully sequenced genomes that are currently determined. However, they promise to become more informative as the number of fully sequenced genomes increases by orders of magnitude.
منابع مشابه
Protein profiling for phylogenetic relationship in snakehead species
Protein banding pattern of eight snakeheads – Channa species viz., Channa striatus, Channa marulius, Channa punctatus, Channa diplogramme, Channa bleheri, Channa gachua, Channa stewartii and Channa aurantimaculata collected from different regions of India were used to study the phylogenetic relationship among them. The banding pattern from muscle protein indicated a unique profile for each spec...
متن کاملProtein profiling for phylogenetic relationship in snakehead species
Protein banding pattern of eight snakeheads – Channa species viz., Channa striatus, Channa marulius, Channa punctatus, Channa diplogramme, Channa bleheri, Channa gachua, Channa stewartii and Channa aurantimaculata collected from different regions of India were used to study the phylogenetic relationship among them. The banding pattern from muscle protein indicated a unique profile for each spec...
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The earliest evidences on circulation of Avian Influenza (AI) virus on the Iranian poultry farms date back to 1998. Great economic losses through dramatic drop in egg production and high mortality rates are characteristically attributed to H9N2 AI virus. In the present work non-structural (NS) genes of 10 Iranian H9N2 chicken AI viruses collected during 1998-2007 were fully sequenced and subjec...
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MOTIVATION Abundance profiling (also called 'phylogenetic profiling') is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads. RESULTS We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP...
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Phylogenetic profiling is a well established method for predicting functional relations and physical interactions between proteins. We present a new method for finding such relations based on phylogenetic profiling of conserved domains rather than proteins, avoiding computationally expensive all versus all sequence comparisons among genomes. The resulting domain interaction map (DIMA) can be ex...
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