Question

color a sequence alignment

2

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9.7 years ago

silvia.caprari84 ▴ 50

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 • 8.9k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by silvia.caprari84 ▴ 50

score 4 · Answer 1 · 2015-03-22

4

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9.7 years ago

venu 7.1k

I think the best and easy way is Jalview

http://www.jalview.org/

ADD COMMENT • link 9.7 years ago by venu 7.1k

Ram · Answer 2 · 2015-03-22

2

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9.7 years ago

Pierre Lindenbaum 164k

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

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Pierre Lindenbaum 164k

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I am using windows. So, How do I run this command?

ADD REPLY • link 9.7 years ago by silvia.caprari84 ▴ 50

1

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You could try Cygwin

ADD REPLY • link 9.7 years ago by kautilya ▴ 430

Ram · Answer 3 · 2015-03-22

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9.7 years ago

thackl ★ 3.0k

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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ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by thackl ★ 3.0k

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this is really nice. Thank you

ADD REPLY • link 9.7 years ago by silvia.caprari84 ▴ 50

Ram · Answer 4 · 2015-03-22

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9.7 years ago

HG ★ 1.2k

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

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by HG ★ 1.2k

Ram · Answer 5 · 2015-03-25

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9.7 years ago

Ian 6.1k

Seaview

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

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Ian 6.1k

score 1 · Answer 6 · 2016-05-13

1

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8.5 years ago

Suzanne ▴ 100

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.

ADD COMMENT • link 8.5 years ago by Suzanne ▴ 100