Evaluation of COMPASS as a comparative mapping tool for ESTs using horse radiation hybrid maps

S. J. Coleman, G. Gong, D. P. Gaile, B. P. Chowdhary, E. Bailey, L. Liu, J. N. MacLeod

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


Loci for 9322 equine expressed sequence tags (ESTs) were predicted using the Comparative Mapping by Annotation and Sequence Similarity (Compass) strategy in order to evaluate the programme's ability to make accurate locus predictions in species with comparative gene maps. Using human genome sequence information from Build 35 (May 2004) and published marker information from the radiation hybrid (RH) maps for equine chromosomes (ECA) 17 and X, 162 ESTs were predicted to locations on ECA17 and 328 ESTs to locations on ECAX by selection of the 'top blast hit'. The locations of 30 ESTs were assessed experimentally by RH mapping analysis to evaluate the accuracy of the Compass predictions. The data revealed that 53% (16 of 30) of the ESTs predicted on ECA17 and ECAX mapped to those chromosomes. Analysis of the results suggested the need to identify expressed orthologous sequences in order to generate more accurate predictions for ESTs. Locus predictions were reassessed with three modifications to the Compass strategy's orthologue selection parameters. Selection of the 'top gene hit' improved accuracy to 72% (21 of 29), while selection of the 'top expressed gene hit' improved accuracy to 86% (24 of 28). Using the default Compass parameters with the UniGene database improved prediction accuracy to 96% (22 of 23); however, this level of accuracy came with a substantial decrease in the total number of predictions. When used with optimized prediction parameters, the Compass strategy can be a practical in silico map location prediction tool for large EST sample sets from unsequenced animal genomes.

Original languageEnglish
Pages (from-to)294-302
Number of pages9
JournalAnimal Genetics
Issue number3
Publication statusPublished - Jun 2007
Externally publishedYes


  • Articular cartilage
  • Comparative gene mapping
  • Equus caballus
  • Expressed sequence tags
  • Radiation hybrid mapping

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Genetics


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