Question: Annotate Multiple Alignment (Clustalw)
2
gravatar for Nicolas Rosewick
7.6 years ago by
Belgium, Brussels
Nicolas Rosewick8.1k wrote:

Hi,

Is there a tool to visualize a multiple alignment produced by clustalw2 with an annotation file (gff3) ?

Thanks

N.

annotation clustalw multiple • 5.1k views
ADD COMMENTlink modified 7 months ago by Hypersphere0 • written 7.6 years ago by Nicolas Rosewick8.1k
1
gravatar for Gjain
7.5 years ago by
Gjain5.3k
Munich, Germany
Gjain5.3k wrote:

Hi,

you might want to try some of the tools listed here: List of alignment visualization software

hope this helps.

ADD COMMENTlink written 7.5 years ago by Gjain5.3k

a specific tool in that list ? :p

ADD REPLYlink written 7.5 years ago by Nicolas Rosewick8.1k

yes you can try Cylindrical BLAST Viewer, MEGA, UGENE

ADD REPLYlink written 7.5 years ago by Gjain5.3k
1
gravatar for SES
7.5 years ago by
SES8.2k
Vancouver, BC
SES8.2k wrote:

UGENE will allow you to annotate an alignment and highlight regions of interest (e.g., intron, UTR, gene). Most of the programs in that list posted by Gjain are for just viewing/editing an alignment. I'll bet Geneious has a really pretty set of buttons you can click to do this as well, but you'll have to buy that software.

ADD COMMENTlink written 7.5 years ago by SES8.2k

I tried ugene now for two hours but I can figure out how to link a gff file to a multiple alignment file ...

ADD REPLYlink written 7.5 years ago by Nicolas Rosewick8.1k

Did you try the add annotations button? You may have to do this manually, and then you can control how the annotations are displayed with the annotations highlighting button.

ADD REPLYlink written 7.5 years ago by SES8.2k
0
gravatar for raunakms
7.5 years ago by
raunakms1.1k
Vancouver, BC, Canada
raunakms1.1k wrote:

I think the best way to do this is using GBrowse !! This tool is handy specially when you are dealing with large dataset or even entire genome !!!

ADD COMMENTlink written 7.5 years ago by raunakms1.1k
0
gravatar for Hypersphere
7 months ago by
Hypersphere0 wrote:

Geneious is my favorite software for all of my bioinformatics needs, including multiple sequence alignments and annotations. It has excellent intuitive tools for adding custom annotations. It is commercial software, but academic licenses are fairly reasonably priced. The software is also cross-platform (Linux, Mac, Windows).

Next best in my opinion is CLC Genomics Workbench. This is commercial software, but many of its features can be accesed for free using "Viewer Mode". In the free viewer mode version, you can do alignments and use the standard annotations, but you cannot edit the annotations or make customized ones.

My university has a site license for DNASTAR Lasergene, but I like Geneious much better.

UGENE is free and has great potential, but it cannot wrap sequence alignments -- this makes UGENE unusable for me.

ADD COMMENTlink written 7 months ago by Hypersphere0
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