Publications

@article{Ramakrishna1999,
title = {Gene identification in bacterial and organellar genomes using GeneScan},
author = {Ramaswamy Ramakrishna and Ramachandran Srinivasan},
url = {https://ramramaswamy.org/papers/071.pdf},
doi = {10.1016/S0097-8485(98)00034-5},
issn = {00978485},
year = {1999},
date = {1999-01-01},
journal = {Computers and Chemistry},
volume = {23},
number = {2},
pages = {165–174},
abstract = {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%). textcopyright 1999 Elsevier Science Ltd. All rights reserved.},
keywords = {Fourier, GeneScan, Haemophilus, Mycoplasma, Plasmodium},
pubstate = {published},
tppubtype = {article}
}

@article{Tiwari1997,
title = {Prediction of probable genes by Fourier analysis of genomic sequences},
author = {S Tiwari, S Ramachandran, S Bhattacharya, A Bhattacharya and R Ramaswamy},
url = {https://doi.org/10.1093/bioinformatics/13.3.263},
doi = {10.1093/bioinformatics/13.3.263},
year = {1997},
date = {1997-06-01},
journal = {Bioinformatics},
volume = {13},
number = {3},
pages = {263–270},
abstract = {Motivation: The major signal in coding regions of genomic sequences is a three-base periodicity. Our aim is to use Fourier techniques to analyse this periodicity, and thereby to develop a tool to recognize coding regions in genomic DNA.

Result: The three-base periodicity in the nucleotide arrangement is evidenced as a sharp peak at frequency f = 1/3 in the Fourier (or power) spectrum. From extensive spectral analysis of DNA sequences of total length over 5.5 million base pairs from a wide variety or organisms (including the human genome), and by separately examining coding and non-coding sequences, we find that the relative height of the peak at f = 1/3 in the Fourier spectrum is a good discriminator of coding potential. This feature is utilized by us to detect probable coding regions in DNA sequences, by examining the local signal-to-noise ratio of the peak within a sliding window. While the overall accuracy is comparable to that of other techniques currently in use, the measure that is presently proposed is independent of training sets or existing database information, and can thus find general application.

Availability: A computer program GeneScan which locates coding open reading frames and exonic regions in genomic sequences has been developed, and is available on request},
keywords = {Fourier, Genes, GeneScan},
pubstate = {published},
tppubtype = {article}
}