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INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms

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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.

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Abbreviations

FPI:

Francisella pathogenicity island

GI:

genomic island

HGT:

horizontal gene transfer

HPI:

high pathogenicity island

INDeGenIUS:

Improved N-mer based Detection of Genomic Islands Using Sequence-clustering

LEE:

locus of enterocyte effacement

LPS:

lipopolysaccharide

MDR:

multidrug resistant

MI:

metabolic island

MoI:

motility island

MSHA:

mannose-sensitive haemagglutinin

PAI:

pathogenicity island

RI:

resistance island

SyI:

symbiotic island

SI:

secretion island

TCA:

tricarboxylic acid

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Authors and Affiliations

  1. Bio-Sciences Division, Innovation Labs, Tata Consultancy Services, 1 Software Units Layout, Hyderabad, 500 081, India

    Sakshi Shrivastava, Ch. V. Siva Kumar Reddy & Sharmila S. Mande

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  1. Sakshi Shrivastava
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  2. Ch. V. Siva Kumar Reddy
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  3. Sharmila S. Mande
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Correspondence to Sharmila S. Mande.

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Shrivastava, S., Siva Kumar Reddy, C.V. & Mande, S.S. INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms. J Biosci 35, 351–364 (2010). https://doi.org/10.1007/s12038-010-0040-4

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