Question: visualizing software for alignment
1
gravatar for kws15
3.5 years ago by
kws1540
kws1540 wrote:

Hi everyone,

basically i am doing some alignment analysis on promoters between two species, this means i will have to analysis quite a lot of gene sequence data (thousands files), i have worked out how meme with the tomtom can give me the ranked motif anlysis result. However, is there anyway that can show the ranked motif on both aligned sequences? ( mene showed the rough position and tomtom only tells the ranked motif). I have written some code in R to show the alignment for the two sequences, but the meme result can hardly be applied in R. I know geneious can show the alignment quite easily and beautifully, is there anyway to combine the geneious and meme analysis together and visuallizing a lot of aligned sequences with highlighted motifs from meme and tomtom results??

Many thanks

alignment geneious meme R • 1.2k views
ADD COMMENTlink modified 2.8 years ago by Suzanne60 • written 3.5 years ago by kws1540
1
gravatar for dago
3.5 years ago by
dago2.5k
Germany
dago2.5k wrote:

Did you look at Jalview?

http://www.jalview.org/

ADD COMMENTlink written 3.5 years ago by dago2.5k
1
gravatar for 5heikki
3.5 years ago by
5heikki8.6k
Finland
5heikki8.6k wrote:

I rather like AliView, although I don't know if it does what you want..

ADD COMMENTlink written 3.5 years ago by 5heikki8.6k
0
gravatar for rse
3.5 years ago by
rse90
Singapore
rse90 wrote:

Try IGV Browser for visualization

ADD COMMENTlink written 3.5 years ago by rse90
0
gravatar for Suzanne
2.8 years ago by
Suzanne60
Dundee, Scotland
Suzanne60 wrote:

Jalview is a free protein and nucleic acid sequence alignment visualisation software. It can be launch from http://www.jalview.org/. There are several Jalview 'how-to' videos on the Jalview YouTube training channel (https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw) you might like to check out.

ADD COMMENTlink written 2.8 years ago by Suzanne60
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