Question

Alternative To Wise2: Other Packages For Mapping Proteins To Genomic And Cdna Sequence Data.

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13.1 years ago

Burlappsack ▴ 690

Hello, I am trying to map a handful of proteins from one species, to the genomic & cDNA sequence of another. I am using the wise2 package, genewiseDB & estwiseDB, for genomic/cdna respectively, and the result is a list of possibly matches and score, their alignments, and a generated cDNA sequence. Although satisfied with wise2, I would like to know: Are there any alternative packages for mapping proteins to genomic DNA/ cDNA that return an alignment? Thank you, Adam

protein genomics cdna • 4.1k views

ADD COMMENT • link updated 13.1 years ago by Lhl ▴ 760 • written 13.1 years ago by Burlappsack ▴ 690

score 2 · Answer 1 · 2011-10-03

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13.1 years ago

lh3 33k

exonerate. Blat can do that, too, but probably not to the sensitivity you want.

ADD COMMENT • link 13.1 years ago by lh3 33k

Ram · Answer 2 · 2012-03-29

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12.7 years ago

Lhl ▴ 760

Spaln http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user.

Is faster and more accurate.

ADD COMMENT • link updated 5.2 years ago by Ram 44k • written 12.7 years ago by Lhl ▴ 760

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yes, based on the comparison they did.

Another one is Genblast, this one is also compared to genewis. You can have a look at the two papers. http://genome.sfu.ca/genblast/

ADD REPLY • link 12.7 years ago by Lhl ▴ 760

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+1 Interesting. Didn't know that. The paper claimed it is better than genewise all around.