onsidered by many experts to have been started to address this very need.
Joo Setubal, associate professor at the Virginia Bioinformatics Institute and the Department of Computer Science at Virginia Tech, commented: "Scientists have known for a long time that publicly available databases of genomes have inconsistencies, errors, and gaps. Some genes are labeled with the wrong function and for others the function is unknown. But nobody had done a systematic study to verify how many genes were simply undetected. This is what we did in our study discover the number of microbial genes that are under the radar."
Scientists have developed different computer tools to help them in their efforts to locate and identify genes. Most of these tools work by building a model based on the features of the sequence and working out the likelihood that an individual segment codes for a gene. Comparing DNA segments with known gene sequences stored in GenBank complements this work. If a DNA segment is similar to the sequence of known genes, then the segment is likely to be a coding gene with a similar function.
Said Setubal, "Such approaches will not find genes that have unusual sequence properties. Furthermore they will not find those genes that have not been detected up to now and hence are not present in GenBank. Our results clearly show that there are many small protein-encoding genes in the genomes of microbes that have been systematically missed."
The lowest estimate in the study placed the number of families of missing genes at 380 in the 780 genomes that were investigated. Said Setubal, "This number is most likely an underestimate since we have been conservative for the criteria we have used for finding these missing gene families."
Wu Feng, associate professor in the Department of Computer Science and the Department of Electrical and Computer Engineering at Virginia Tech, remarked: "To facilitate the rapid discovery of missing gene
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| Contact: Barry Whyte whyte@vbi.vt.edu 540-231-1767 Virginia Tech Source:Eurekalert |
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