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Old 01-19-2012, 11:45 AM   #1
ssully
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Default Publication-quality graphics program for chromosome-length sequences?

I'm in dire need of free/cheap software that does something I think is simple, but seems to be rare (without paying through the nose).

I just want to be able to input a long sequence (or sequences) and a list of features and coordinates, and output a publication-quality graphic of the sequence as a line or rectangular box, with the features accurately mapped onto it as different shapes/colors. And I'd like the output to be proportional, so that if sequence A is 2 millions bases and sequence B is 1 million, the first line will be twice as long as the second.

Packages I've looked at so far, which seem geared for plasmids, fall down in one or more of these criteria. Any suggestions?
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Old 01-19-2012, 12:40 PM   #2
wahoosteve
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If you're comfortable with python scripting, you may be able to do something like this with the GenomeDiagram or BasicChromosome modules within the BioPython package (I haven't done this myself). http://news.open-bio.org/news/2011/1...-in-biopython/
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Old 01-19-2012, 02:01 PM   #3
ssully
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I'm not (comfortable with python scripting) but thanks anyway.
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Old 01-19-2012, 02:15 PM   #4
ECO
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Try Genious. There is a free trial and in general it seems to handle visualization of features ON sequences pretty well.

A more difficult route is something like IGV where you can define your features in a bed file and view them in different ways.

Both these methods will at some point require a high-res screenshot for output as far as I know.
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Old 01-20-2012, 05:24 AM   #5
Jim Robinson
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If you try IGV output the result as an SVG file (File > Save Image... -> type = svg).
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