Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Methods. 2009 Sep;49(1):50-5. doi: 10.1016/j.ymeth.2009.05.010. Epub 2009 May 23.

Bioinformatic approaches to identifying orthologs and assessing evolutionary relationships.

Author information

  • Division of Neurosciences, New England Primate Research Center, Harvard Medical School, Pine Hill Drive, Southborough Campus, Southborough, MA 01772, USA. eric_vallender@hms.harvard.edu

Abstract

Non-human primate genetic research defines itself through comparisons to humans; few other species require the implicit comparative genomics approaches. Because of this, errors in the identification of non-human primate orthologs can have profound effects. Gene prediction algorithms can and have produced false transcripts that have become incorporated into commonly used databases and genomics portals. These false transcripts can arise from deficiencies in the algorithms themselves as well as through gaps and other problems in the genome assembly. Putative genes generated can not only miss microexons, but improperly incorporate non-coding sequence resulting in pseudogenes or other transcripts without biological relevance. False transcripts then become identified as orthologs to established human genes and are too often taken as gospel by unwary researchers. Here, the processes through which these errors propagate are isolated and methods are described for identifying false orthologs in databases with several representative errors illustrated. Through these steps any researcher seeking to make use of non-human primate genetic information will have the tools at their disposal to ascertain where errors exist and to remedy them once encountered.

PMID:
19467333
[PubMed - indexed for MEDLINE]
PMCID:
PMC2732758
Free PMC Article

Images from this publication.See all images (4)Free text

Figure 1
Figure 2
Figure 3
Figure 4
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for Elsevier Science Icon for PubMed Central
    Loading ...
    Write to the Help Desk