International Journal of Information Engineering and Electronic Business (IJIEEB)
IJIEEB Vol. 7, No. 2, 8 Mar. 2015
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Phylogenetic Method for High-Throughput Ortholog Detection
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Author(s)
Shaifu Gupta
1,*
Manpreet Singh
1
Index Terms
Orthologs, comparative genomics, Phylogenetics, Species-overlap, Patristic distance
Abstract
Accurate detection of orthologous proteins is a key aspect of comparative genomics. Orthologs in different species can be used to predict the function of uncontrived genes from model organisms as they retain the same biological function through the path of evolution. Orthologs can be inferred using phylogenetic, pair-wise similarity or synteny based methods. The study here describes a computational method for detecting orthologs of a protein. A phylogenetic tree based approach is used for identification of orthologous proteins. A Combination of species overlap algorithm and patristic distances is used for detecting orthologs of a protein from a set of FASTA sequences. Patristic distances have been used to drill the orthology predictions of any protein down to its closest orthologs. The approach gives a considerably good accuracy and has high specificity and precision. The use of Distance threshold allows controlling the stringency level of predictions so that the closeness and proximity between the protein of interest and its orthologs can be adjusted.
Cite This Paper
Shaifu Gupta, Manpreet Singh, "Phylogenetic Method for High-Throughput Ortholog Detection", International Journal of Information Engineering and Electronic Business(IJIEEB), vol.7, no.2, pp.51-59, 2015. DOI:10.5815/ijieeb.2015.02.07
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