Question

How to make a Multiple-sequence alignment representation figure like this

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7.5 years ago

xyc_liang • 0

Use red bars and black bars represent the non-synonymous and synonymous mutations in the alignment. Blanks indicate deletion. Is there any program or script could make it?

just like fig.1 in this paper http://www.pnas.org/content/106/23/9519.long

alignment • 2.2k views

ADD COMMENT • link updated 7.5 years ago by EVR ▴ 610 • written 7.5 years ago by xyc_liang • 0

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Schematic representation of sequence alignment

ADD REPLY • link 7.5 years ago by xyc_liang • 0

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Paper describes using ClustalX and GeneDoc which are both free programs. Many figures are post-processed using an image editor so you may not be able to get the exact result you see in a paper from just the programs mentioned.

ADD REPLY • link 7.5 years ago by GenoMax 141k

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I get it. I just like the style. Another paper published by their group mentioned that the representation was generated by a home-made PERL script. So I wonder is there anyone has this type of program or script?

ADD REPLY • link 7.5 years ago by xyc_liang • 0

score 0 · Answer 1 · 2016-10-25

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7.5 years ago

EVR ▴ 610

Use software ClustalX to generate the exact figure like in paper

ADD COMMENT • link 7.5 years ago by EVR ▴ 610

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The alignment was performed by ClustalX, but the schematic representation of sequence alignment was generated by some other programs or scripts.

ADD REPLY • link 7.5 years ago by xyc_liang • 0