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The Best Algorithm/Program For Pairwise Alignment Of Long Sequences (>100Kb)

I am trying to align many human and mouse genes. Many of the genes are longer than 100kb. Programs like Muscle are not able to align such long sequences because they run short of memory. I have also tried ACANA, which is fast enough, but I get a very low identity percentage between the two sequences.

What program do you suggest that combines accuracy with efficiency and speed?

algorithm sequence alignment pairwise
• 5,673 views • link
updated by Ram Ram • written by Ali R. Vahdati Ali R. Vahdati

Blastz and patternhunter; perhaps also cross_match.

• 106 views • link
updated by Ram Ram • written by lh3 lh3

2 answers

I would recommend exonerate, which performs pairwise alignment using dynamic programming with heuristic approximations.

• 81 views • link
updated by Ram Ram • written by Botond Sipos Botond Sipos

I tried exonerate using exhaustive global alignment option. This procedure, although not requiring a lot of memory, takes a LONG time.

• 0 views • link
updated by Ram Ram • written by Ali R. Vahdati Ali R. Vahdati

I have ended up using AVID program. It is fast and memory efficient in doing global alignments. The quality of alignments are comparable with Muscle.

• 34 views • link
updated by Ram Ram • written by Ali R. Vahdati Ali R. Vahdati

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