4 - Central Institute of Brackishwater Aquaculture
4 - Central Institute of Brackishwater Aquaculture
4 - Central Institute of Brackishwater Aquaculture
Create successful ePaper yourself
Turn your PDF publications into a flip-book with our unique Google optimized e-Paper software.
Natlonal workshop-cum-Training on Bioinform8tia and Intorm8tion Management in <strong>Aquaculture</strong><br />
pylori [Sakharkar et al., 2004; Dutta et al., 20061. The work has been effectively<br />
complemented with the compilation <strong>of</strong> the Database <strong>of</strong> Essential Genes (DEG) for<br />
a number <strong>of</strong> pathogenic micro-organims[Zhang et al., 20041.<br />
2. Materials and methods<br />
2.1 Identification Novel Drug Targets: Whole genome sequences <strong>of</strong> four<br />
strains <strong>of</strong> C. pneurnoniae (C. pneumoniae AR39, C. pneurnoniae 3138, C.<br />
pneurnoniae TW1839 and C, pneurnoniae CW1029) were downloaded from the<br />
National Center for Biotechnology Information (NCBI)<br />
(ft~://ft~.ncbi.nlm. nih.aov/aenomes/bactera). The strains are having a circular<br />
genome with 1052-1112 predicted protein coding sequences [Kaiman et al.,<br />
19991. From the complete genome sequences data, the genes whose sequence<br />
length is greater than 100 amino acids were selected out. These selected genes<br />
were then subjected to BLASTX against the DEG database<br />
(htt~://tubic.tiu.edu.cu.deq) to screen out essential genes. A random<br />
expectation value (E-value) cut-<strong>of</strong>f <strong>of</strong> 10.'~~ and a minimum bit-score cut-<strong>of</strong>f <strong>of</strong><br />
100 were used [Dutta et dl., 20061. The screened essential genes <strong>of</strong> C.<br />
pneumoniae were then subjected to BLASTX against the human genome to<br />
identify the non-human homologous proteins in the bacteria. The homologous<br />
were excluded and the list <strong>of</strong> non-homologous was compiled. The identified<br />
essential non-human homologous proteins were then classified into different<br />
groups based on biological function with the help <strong>of</strong> the Swiss-Prot Protein<br />
Database (~tt~://us.ex~asv.ora/s~rot;). The classified essential and non-human<br />
homologous proteins within the same function group were further analyzed to<br />
find highly conserved proteins common to all four C, pneurnoniae strains by<br />
using MSA (Multiple Sequence Alignment) in ClustalX [Thompson et al., 19971.<br />
These proteins are considered as common drug target for all four C. pneumoniae<br />
strains. The flow chart <strong>of</strong> the process is shown in the Figure-1.
Change language