Not Everyone Hits It Out of the Ballpark

Keith Robison is irked by a bad paper, which he reviews at Omics! Omics! The paper in question uses comparative genomic analysis of chimp and human kinases and erroneously (according to Robison) discovers several "novel" chimpanzee kinases with no close counterpart in human. For instance, the authors find one that they describe as a specific protein based on 31-percent sequence homology. "Finding a human-mouse ortholog identity of less than 31% would be stunning; for human-chimp it would be indescribably surprising." Robison does a little sleuthing of his own, plugging the ORF sequence into the RefSeq human protein dataset and comes up with a new protein with close to 90 percent similarity. "A strong criticism of mine of this paper is that it relies too much on Ensembl-derived sequences and annotation. Ensembl is a great system & I have high respect for it, but it is also trying to do the very complex job of integrating a lot of other data with genomic sequences of varying quality and we are not scientists if we fully trust it to always be correct." Robison offers some tips on how to improve the analysis, the two biggest being that scientists need to keep in mind that genomes are draft sequences only and that they always need to apply appropriate computational controls.