Question

Annotate Multiple Alignment (Clustalw)

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12.7 years ago

Nicolas Rosewick 11k

Hi,

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

Thanks

N.

clustalw annotation multiple • 9.5k views

ADD COMMENT • link updated 5.8 years ago by Hypersphere • 0 • written 12.7 years ago by Nicolas Rosewick 11k

score 1 · Answer 1 · 2012-03-01

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12.7 years ago

Gjain 5.8k

Hi,

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

hope this helps.

ADD COMMENT • link 12.7 years ago by Gjain 5.8k

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a specific tool in that list ? :p

ADD REPLY • link 12.7 years ago by Nicolas Rosewick 11k

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yes you can try Cylindrical BLAST Viewer, MEGA, UGENE

ADD REPLY • link 12.7 years ago by Gjain 5.8k

score 1 · Answer 2 · 2012-03-01

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12.7 years ago

SES 8.6k

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 COMMENT • link 12.7 years ago by SES 8.6k

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

ADD REPLY • link 12.7 years ago by Nicolas Rosewick 11k

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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 REPLY • link 12.7 years ago by SES 8.6k

score 0 · Answer 3 · 2012-03-30

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12.7 years ago

raunakms ★ 1.1k

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 COMMENT • link 12.7 years ago by raunakms ★ 1.1k

score 0 · Answer 4 · 2019-02-02

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.