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color a sequence alignment

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
• 10,278 views • link
updated by Ram Ram • written by silvia.caprari84 • silvia.caprari84

6 answers

I think the best and easy way is Jalview

http://www.jalview.org/

• 0 views • link
written by venu venu

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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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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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updated by Ram Ram • written by thackl thackl

Have a look: http://multalin.toulouse.inra.fr/multalin/multalin.html

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updated by Ram Ram • written by HG HG

Seaview

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

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updated by Ram Ram • written by Ian Ian

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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written by Suzanne Suzanne

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