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

Question

[Burlappsack]

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

Answer 1

[lh3]

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

Answer 2

[Lhl]

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

Is faster and more accurate.

[Lhl]

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/

[lh3]

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

[Lhl]

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