color a sequence alignment
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7.5 years ago

Hi,

do you know a tool (server) that colors a sequence alignment file (in FASTA format) by residue type?

Thank you very much

Silvia

alignment • 7.4k views
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7.5 years ago
venu 7.0k

I think the best and easy way is Jalview

http://www.jalview.org/

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7.5 years ago

Using sed

(echo "<body><html><pre>" && curl -s http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/apoex.fa | sed -r -e '/^[^>]/s%([ALVLIFLP])%\1%g' -e 's/^>/\>/' && echo "</pre></body></html>" ) > out.html
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I am using windows. So, How do I run this command?

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You could try Cygwin

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7.5 years ago
thackl ★ 2.9k

If you need it for presentations, papers, etc., there is a very nice LaTeX package: http://www.uni-kiel.de/Pharmazie/chem/Prof_Beitz/pdf/texshade.pdf

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this is really nice. Thank you

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7.5 years ago
Ian 5.9k

Seaview

Colours residue based on different properties and has various output types. It has many other sequence functions too.

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6.4 years ago
Suzanne ▴ 80

Jalview www.jalview.org) has many option for colouring whole alignments or groups. I have added the link to a youtube video about this. Plus there are videos about how to change the appearance of the alignment and exporting journal quality figures.

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