Gene identification in bacterial and organellar genomes using GeneScan

Ramakrishna, Ramaswamy ; Srinivasan, Ramachandran (1999) Gene identification in bacterial and organellar genomes using GeneScan Computers & Chemistry, 23 (2). pp. 165-174. ISSN 0097-8485

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The performance of the GeneScan algorithm for gene identification has been improved by incorporation of a directed iterative scanning procedure. Application is made here to the cases of bacterial and organnellar genomes. The sensitivity of gene identification was 100% in Plasmodium falciparum plastid-like genome (35 kb) and in 98% in the Mycoplasma genitalium genome (580 kb) and the Haemophilus influenzae Rd genome (1.8 Mb). Sensitivity was found to improve in both the Open Reading Frames (ORFs) which have been identified as genes (by homology or by other methods) and those that are classified as hypothetical. False positive assignments (at the nucleotide level) were 0.25% in H. influenzae genome and 0.3% in M. genitalium. There were no false positive assignments in the plastid-like genome. The agreement between the GeneScan predictions and GeneMark predictions of putative ORFs was 97% in M. genitalium genome and 86% in H. influenzae genome. In terms of an exact match between predicted genes/ORFs and the annotation in the databank, GeneScan performance was evaluated to be between 72% and 90% in different genomes. We predict five putative ORFs that were not annotated earlier in the GenBank files for both M. genitalium and H. influenzae genomes. Our preliminary analysis of the newly sequenced G+C rich genome of Mycobacterium tuberculosis H37Rv also shows comparable sensitivity (99%).

Item Type:Article
Source:Copyright of this article belongs to Elsevier Science.
Keywords:Genescan; Mycoplasma; Plasmodium; Haemophilus; Fourier
ID Code:45363
Deposited On:28 Jun 2011 04:50
Last Modified:28 Jun 2011 04:50

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