Question: How Can I Perform Multiple Local Alignments In Jalview?
gravatar for JacobS
7.3 years ago by
Cleveland, Ohio
JacobS940 wrote:

I often use Jalview for global alignment of proteins or DNA sequences for analyzing homologs, etc. However, I would like to be able to visualize many local alignments at once. For example, if I have a specific gene region, say 20KB, and I know that there are 10 genes within the region, each 1 KB. I would like to be able to input the 20KB region and all 10 genes into Jalview, and conduct local alignments of each gene to the reference at once, so I can see where the genes are aligning to the gene region. Does anyone know how to do this in Jalview in particular? Thanks!

ADD COMMENTlink modified 5.7 years ago by Foreveremain60 • written 7.3 years ago by JacobS940

I am not sure that you can do this with JalView currently. You might want to ask on the JalView mailing lists (see to see if anyone knows of a good way to do this with JalView.

ADD REPLYlink written 7.2 years ago by Hamish3.2k
gravatar for Foreveremain
5.7 years ago by
United Kingdom
Foreveremain60 wrote:

We are working on supporting exonerate ( output in Jalview, and may well provide it as a service in the future. Until then, you could try using one of the alignment services which allows local alignment by setting the 'end gaps' cost to zero (ClustalWS does this, and MAFFT has a local alignment mode too). For DNA, I'd also recommend picking the IDENTITY substitution matrix in ClustalWS since you don't expect much variation.

Jalview's built in alignment algorithms could easily be adapted for this too. I've added a feature request over at


ADD COMMENTlink written 5.7 years ago by Foreveremain60
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