Question: The Best Algorithm/Program For Pairwise Alignment Of Long Sequences (>100Kb)
2
gravatar for Ali R. Vahdati
6.7 years ago by
Zurich, Switzerland
Ali R. Vahdati190 wrote:

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?

ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 6.7 years ago by Ali R. Vahdati190
2

Blastz and patternhunter; perhaps also cross_match.

ADD REPLYlink written 6.7 years ago by lh331k
2
gravatar for Botond Sipos
6.7 years ago by
Botond Sipos1.7k
United Kingdom
Botond Sipos1.7k wrote:

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

ADD COMMENTlink written 6.7 years ago by Botond Sipos1.7k

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

ADD REPLYlink modified 6.4 years ago • written 6.7 years ago by Ali R. Vahdati190
2
gravatar for Ali R. Vahdati
6.7 years ago by
Zurich, Switzerland
Ali R. Vahdati190 wrote:

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.

ADD COMMENTlink written 6.7 years ago by Ali R. Vahdati190
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