LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA

Table 4.

Percentage of Exons Correctly Aligned During the CHAOS-Based Anchoring Phase of LAGAN (Steps 1,2)

Alignment human vs. 90%–100% 50%–89% 10%–49% 0%–9%
default transl. default transl. default transl. default transl.
Chimpanzee 97 97 3 3 0 0 0 0
Baboon 77 77 21 21 3 3 0 0
Cow 21 21 43 43 36 36 0 0
Pig 19 19 33 30 47 50 1 1
Dog 20 20 37 37 41 42 2 1
Cat 20 20 41 41 39 39 0 0
Mouse 10 10 35 37 52 51 2 2
Rat 13 10 47 46 40 42 1 2
Chicken 9 9 26 41 62 47 3 3
Fugu 12 29 19 29 57 35 12 7
Zebrafish 27 33 29 42 38 25 4 0

  • Percentage of human exons that have a given proportion of their lengths covered (90%–100%, 50%–89%, 10%–49%, and 0%–9%). Translated anchoring performs better at covering a greater proportion of exons. However, we do not have measurements on whether translated anchoring performs worse in covering biologically significant noncoding features.

This Article

  1. Published in Advance March 12, 2003, doi: 10.1101/gr.926603 Genome Res. 13: 721-731

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