Gene finding

With the advent of sequenced genomes, identifying the genes encoded in the genome has become a major research effort. The programs described next are currently the 

In Silico Technologies in Drug Target Identification and Validation 

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The TIGR has software systems available for free download. These include software for gene finding/annotation, alignment, sequencing/finishing, and microarray analysis. All of them are OSI (Open Source Initiative) Certified Open Source Software. 

The Cryptocercus punctatus wood-feeding cockroach complex in the eastern United States was recently revised based on cuticular hydrocarbon profiles, chromosome count and DNA sequencing (16S and COII mitochondrial genes and ITS nuclear gene). Findings showed that there were five distinct hydrocarbon phenotypes that were not... 

RNA Gene finding/annotation RNAa libraries, with variations for, for example, identifying UTRs multimapped reads, novel gene models, and multiple isoforms present challenges... 

It was concluded that 99.24% of the splice site pairs should be GT-AG, 0.69% GC-AG, 0.05% AT-AC and finally only 0.02% could consist of other types of non-canonical splice sites (Table 3.3). Therefore, gene finding approaches using just standard GT-AG splice sites can potentially predict accurately 97% genes (assuming 4-5 exons per gene on average). If the... 

Performance of multiple gene-finding for 38 genomic sequences. Me is missing exons and W is wrong exons. M r lines provide predictions on sequences with masked repeats. Sn o is exon prediction accuracy including overlapping exons. 

Internet sites for gene finding and functional site prediction... 

Salamov A., Solovyev V. (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Research 10, 516-522. 

Krog A. (1997) Two methods for improving performance of an HMM and their application for gene finding. Ismb., 5, 179-186. 

Korf, I. (2004) Gene finding in novel genomes. BMC Bioinformatics 5, 59. 

Key Words Noncoding RNA gene finding conserved RNA secondary structure RNA structure prediction. 

Disease selection Similarity searching Splice variants Mining expression data Literature searching Mining SNP studies Gene finding EST identification... 

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