Table 1.
Evaluating eShadow's Performance on Recapitulating Human/Mouse Conservation Patterns in Human/Baboon Alignments
|
Detected coding exons
|
|||||
|---|---|---|---|---|---|
| Gene locus | Sensitivity | Specificity | Common region lengtha | All | >150 bp |
| WNT2 | 67.9% | 61.1% | 52.8 kb | 5/5 | 4/4 |
| CECR | 55.7% | 82.5% | 63.4 kb | 7/20 | 5/7 |
| PCQAP | 51.1% | 89.8% | 123.4 kb | 13/20 | 8/8 |
| SNAP29 | 46.0% | 89.6% | 125.1 kb | 19/27 | 7/10 |
| TCF4 | 61.4% | 56.7% | 137.8 kb | 10/11 | 1/1 |
| Average | 59.3% | 77.6% | 100.5 kb | 54/87 (62%) | 25/30 (83%) |
Sequences for the WNT2 region were obtained by excising ∼53 kb from the ∼2 Mb region [NISC Comparative Sequencing Program has sequenced for the CFTR locus sequencing project (Thomas et al., 2003)]. A total of four baboon BACs spanning CECR, PCQAP, SNAP29, and TCF4 gene loci were downloaded from NCBI (Accession nos. AC091672, AC128639, AC129881, AC113267). Human and mouse sequences were obtained from UCSC database.
a
Common region lengths are defined as regions of homology (kb) flanked by at least one ECR and one HMMI prediction. HMMI parameters used: 0.98/0.90/0.005.