Browsing by Subject "MEME"

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    Studying molecular evolution using tools of bioinformatics: an example from maize starch biosynthetic pathway
    (University of North Bengal, 2011-03) Ghatak, V; Ghosh, PD
    Various tools and techniques of bioinformatics are used to reveal the evolutionary pattern and chronology of different phylogenetic events in the evolutionary history of an organism. n maize, shrunken, brittle, waxy and sugary mutants all results from anomalies in the starch biosynthetic pathway. The genes responsible are shl, bt2,wxl and sul respectively. The present article explores and depicts an outline of computer application based methods adopted in a standard molecular phylogenetic analysis using sequence data of these gene products controlling different steps of maize starch biosynthetic pathway. Several such methods namely MSA, PSI-BLAST, Maximum Likelihood analysis and UPGMA analysis reveals that shrunkenl, waxyl and sugaryl have evolutionary rates ranging in between 0.001-0.003 substitutions per Site. Non-synonymous substitution (as polymorphism is analysed using protein sequences) substitution rate is much slower in brittle2 (0.0006). The divergence times between the ancestors of Sorghum and Maize teosinte lineage has been calculated from these non-synonymous substitution rates. MEME analyses and distribution of motifs in these sequences and their homologues suggest changes (duplication and rearrangements) in the genetic material after Sorghum-maize split.