INDeGenIUS,a new method for high-throughput identification of specialized functional islands in completely sequenced organisms |
| |
Authors: | Sakshi Shrivastava Ch V Siva Kumar Reddy Sharmila S Mande |
| |
Institution: | (1) Bio-Sciences Division, Innovation Labs, Tata Consultancy Services, 1 Software Units Layout, Hyderabad, 500 081, India; |
| |
Abstract: | Genomic islands (GIs) are regions in the genome which are believed to have been acquired via horizontal gene transfer events
and are thus likely to be compositionally distinct from the rest of the genome. Majority of the genes located in a GI encode
a particular function. Depending on the genes they encode, GIs can be classified into various categories, such as ‘metabolic
islands’, ‘symbiotic islands’, ‘resistance islands’, ‘pathogenicity islands’, etc. The computational process for GI detection
is known and many algorithms for the same are available. We present a new method termed as Improved N-mer based Detection
of Genomic Islands Using Sequence-clustering (INDeGenIUS) for the identification of GIs. This method was applied to 400 completely
sequenced species belonging to proteobacteria. Based on the genes encoded in the identified GIs, the GIs were grouped into
6 categories: metabolic islands, symbiotic islands, resistance islands, secretion islands, pathogenicity islands and motility
islands. Several new islands of interest which had previously been missed out by earlier algorithms were picked up as GIs
by INDeGenIUS. The present algorithm has potential application in the identification of functionally relevant GIs in the large
number of genomes that are being sequenced. Investigation of the predicted GIs in pathogens may lead to identification of
potential drug/vaccine candidates. |
| |
Keywords: | |
本文献已被 SpringerLink 等数据库收录! |
|