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a database for Mycobacterium secretome analysis
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Analysis

  • Whole genome sequence of 21 Mycobacterium strains were downloaded from the Integrated Microbial Genome Database (www. img.jgi.doe.gov/) Signal peptides were predicted using various software like SignalP, PredLipo, TATFIND etc.
  • The signal peptide containing proteins were sorted into different COG categories.
  • CAI calculation of all the three different types of signal peptides has been done for all genomes.
  • G+C content of the whole genome sequence was calculated
  • calculation of other indices like CBI, Fop, GC3s, Nc etc are done to access the degree and direction of codon bias and to analyse the codon usage pattern. GC3s symbolize the frequency of guanine and cytosine at the synonymous third positions of codons
  • Correspondence analysis between protein coding genes, ribosomal genes and signal peptides is done to analyse the quantity of expression of genes
  • BioPerl script was used to identify potential orthologous protein from all the Mycobacterium strains . The core secretome was identified 
  • The rate of evolution of secretory protein was estimated by considering The ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitution rates.
  • The codon usage and expression pattern analysis data was gathered.
  • All the relevant graphs was created .
  • Sequence logo graph has been done by using weblogo server.

©2011 All Rights reserved. Designed by: Astami and Sangeeta

 

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