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Old 08-07-2008, 01:00 PM   #51
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Location: Boston

Join Date: Feb 2008
Posts: 693

Another good program: ZOOM! Zillions of oligos mapped, which is online now at Bioinformatics. ZOOM resembles Eland a lot, but it further improves the spaced-seed method. I think SOLiD read mapper also uses quite a similar strategy of spaced seed, but it indexes genome, while ZOOM indexes reads like Eland.

Also, I believe ZOOM is carefully engineered. Outperforming eland with a similar algorithm is non-trivial, even given the advantages in the algorithm. I just wonder how ZOOM-C/I/P may perform. The authors did not give benchmark.

Last edited by lh3; 08-07-2008 at 01:04 PM.
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