Tech, Maike and Merkl, Rainer (2003) YACOP: Enhanced gene prediction obtained by a combination of existing methods. In Silico Biology 3 (4), pp. 441-451.
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Other URL: http://www.bioinfo.de/isb/2003030037/
The performance of gene-predicting tools varies considerably if evaluated with respect to the parameters sensitivity and specificity or their capability to identify the correct start codon. We were interested to validate tools for gene prediction and to implement a metatool named YACOP, which combines existing tools and has a higher performance. YACOP parses and combines the output of the three gene-predicting systems Criticia, Glimmer and ZCURVE. It outperforms each of the programs tested with its high sensitivity and specificity values combined with a larger number of correctly predicted gene starts. Performance of YACOP and the gene-finding programs was tested by comparing their output with a carefully selected set of annotated genomes. We found that the problem of identifying genes in prokaryotic genomes by means of computational analysis was solved satisfactorily. In contrast, the correct localization of the start codon still appeared to be a problem, as in all cases under test at least 7.8% and up to 32.3% of the positions given in the annotations differed from the locus predicted by any of the programs tested. YACOP can be downloaded from http://www.g2l.bio.uni-goettingen.de.
|Institutions:||Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Reinhard Sterner > Arbeitsgruppe PD Dr. Rainer Merkl|
|Keywords:||Algorithms Codon, Initiator/genetics Databases, Genetic Escherichia coli/genetics Genes, Bacterial *Genetic Techniques Genomics/statistics & numerical data Research Support, Non-U.S. Gov't Salmonella typhimurium/genetics *Software|
|Subjects:||500 Science > 570 Life sciences|
|Refereed:||Yes, this version has been refereed|
|Created at the University of Regensburg:||No|
|Deposited On:||13 Nov 2009 12:15|
|Last Modified:||21 Dec 2009 07:46|