Table 1

Effect of the chain-net approach on the translated BLAT alignments

Alignment

Chain&Net

Alignments

Genomic Coverage

Coding Exon Coverage


Human-Chicken

NO

894342

39885438

1.09%

20286249

49.55%


Human-Chicken

YES

337551

39928606

1.09%

20024694

48.91%


Human-C.savignyi

NO

142111

6039918

0.16%

4227643

10.33%


Human-C.savignyi

YES

54447

5720330

0.16%

4052706

9.90%


Mouse-Tetraodon

NO

509589

20480760

0.75%

14931981

42.29%


Mouse-Tetraodon

YES

177447

19615452

0.72%

14450833

40.93%


Mouse-Xenopus

NO

2061217

29538379

1.09%

18769694

53.16%


Mouse-Xenopus

YES

239083

27926452

1.03%

18113364

51.30%


This table compares the result of the translated BLAT alignmnts before and after using the chain-net approach. While the total number of alignments is reduced to less than 40%, the coverage is only slightly reduced.

Severin et al. BMC Bioinformatics 2010 11:240   doi:10.1186/1471-2105-11-240

Open Data