Looking for an annotation-aware sequence alignment visualization tool
0
1
Entering edit mode
4.3 years ago
changxu.fan ▴ 70

I'm trying to do a very simple thing: align 5 genes (exons + introns). Currently what I do is: align them with stretcher (EMBL-EBI) -> visualize with Jalview -> annotate exons and introns by hand.

My problem is that this is highly inefficient and I tend to mess up somewhere. Also, I need to re-annotate them every time I re-generate the alignment as a result of parameter tuning.

I was wondering if there is an alignment/visualization tool that can take into account the annotation information that can be supplied as, for example, a bed file. And "lift over" the annotation in the bed file to the alignment during visualization.

Thank you so much~

alignment genome jalview • 886 views
ADD COMMENT
1
Entering edit mode

IGV?

ADD REPLY

Login before adding your answer.

Traffic: 1551 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6