An unsupervised classification scheme for improving predictions of prokaryotic TIS

BMC Bioinformatics
Maike Tech, Peter Meinicke

Abstract

Although it is not difficult for state-of-the-art gene finders to identify coding regions in prokaryotic genomes, exact prediction of the corresponding translation initiation sites (TIS) is still a challenging problem. Recently a number of post-processing tools have been proposed for improving the annotation of prokaryotic TIS. However, inherent difficulties of these approaches arise from the considerable variation of TIS characteristics across different species. Therefore prior assumptions about the properties of prokaryotic gene starts may cause suboptimal predictions for newly sequenced genomes with TIS signals differing from those of well-investigated genomes. We introduce a clustering algorithm for completely unsupervised scoring of potential TIS, based on positionally smoothed probability matrices. The algorithm requires an initial gene prediction and the genomic sequence of the organism to perform the reannotation. As compared with other methods for improving predictions of gene starts in bacterial genomes, our approach is not based on any specific assumptions about prokaryotic TIS. Despite the generality of the underlying algorithm, the prediction rate of our method is competitive on experimentally verified test data fr...Continue Reading

References

Jun 3, 1988·Science·J A Swets
Apr 1, 1974·Proceedings of the National Academy of Sciences of the United States of America·J Shine, L Dalgarno
Sep 5, 1997·Science·F R BlattnerY Shao
Nov 6, 1998·Neural Computation·A Utsugi
Aug 14, 1999·Nucleic Acids Research·S S HannenhalliJ W Fickett
Nov 11, 1999·Nucleic Acids Research·A L DelcherS L Salzberg
Dec 11, 1999·Nucleic Acids Research·K E Rudd
Jul 28, 2001·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·T YadaK Nakai
Dec 26, 2001·Bioinformatics·B E SuzekS L Salzberg
Feb 2, 2002·Nature·M SalanoubatC A Boucher
Mar 11, 2003·Nucleic Acids Research·Feng-Biao GuoChun-Ting Zhang
Dec 23, 2003·The International Journal of Biochemistry & Cell Biology·Hong-Yu OuChun-Ting Zhang
Sep 21, 2004·Proceedings of the National Academy of Sciences of the United States of America·Matthew T G HoldenJulian Parkhill

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Citations

May 4, 2010·Nature Methods·Amrita PatiNikos C Kyrpides
May 20, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·F Robert TabitaNathan E Kreel
Dec 22, 2007·International Journal of Neural Systems·Britta MerschChristian Igel
Mar 28, 2008·BMC Bioinformatics·Gang-Qing HuZhen-Su She
Apr 30, 2008·BMC Bioinformatics·Katharina J HoffPeter Meinicke
Sep 20, 2008·BMC Bioinformatics·Michael E Sparks, Volker Brendel
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Tahir MehmoodLars Snipen
Oct 21, 2009·Journal of Theoretical Biology·Tingting GaoLing Jing
May 10, 2018·Journal of Bioinformatics and Computational Biology·Oxana A VolkovaRuslan N Sharipov
Jul 4, 2012·Journal of Biosciences·Garima KhandelwalB Jayaram

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Software Mentioned

GS
Start
TICO
TIs COrrector
GLIMMER2
RBSfinder
Finder
Artemis Comparative Tool
MED
FrameD

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