Question: Alternative To Wise2: Other Packages For Mapping Proteins To Genomic And Cdna Sequence Data.
1
gravatar for Burlappsack
7.6 years ago by
Burlappsack660
Burlappsack660 wrote:

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

cdna protein genomics • 2.2k views
ADD COMMENTlink written 7.6 years ago by Burlappsack660
2
gravatar for lh3
7.6 years ago by
lh331k
United States
lh331k wrote:

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

ADD COMMENTlink written 7.6 years ago by lh331k
2
gravatar for Lhl
7.1 years ago by
Lhl730
United States
Lhl730 wrote:

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

Is faster and more accurate.

ADD COMMENTlink written 7.1 years ago by Lhl730
1

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 REPLYlink written 7.1 years ago by Lhl730

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

ADD REPLYlink written 7.1 years ago by lh331k

But i do not mean genblast is comparable/similar to genewise.

ADD REPLYlink written 7.1 years ago by Lhl730
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