visualizing software for alignment
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5.5 years ago
kws15 ▴ 40

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

R geneious meme alignment • 1.8k views
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5.5 years ago
dago ★ 2.7k

Did you look at Jalview?

http://www.jalview.org/

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5.5 years ago
5heikki 10k

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

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5.5 years ago
rse ▴ 90

Try IGV Browser for visualization

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4.8 years ago
Suzanne ▴ 80

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.

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