GMV FAQ

General Questions
Platform specific FAQ
Building GMV
- What kind of platforms are supported?
- Which version of GTK+ is required?

General Questions †

What GMV can do? †

GMV is a comparative genome browser, to explore the results from Murasaki. It can load Murasaki's results, genome sequences and their annotations. GMV has several filtering and reporting features, to help genome wide studies.

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Can I try GMV (and murasaki) by just downloading the software? †

If you're using MacOS X or Microsoft Windows, yes. Please go to the download section of GMV mainpage.

Also, Murasaki binary for MacOS X 10.5 is available at my personal website. There is no pre-built Murasaki binary for other platforms.

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Is GMV able to visualize non-Murasaki results from BLASTZ, Mauve etc.? †

No. But there are some converter scripts (ex: mauve2anchors.pl) are included in Murasaki's tarball. You may be able to visualize Mauve and other tools' results by converting them into ".anchors" and ".seqs" format of Murasaki.

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There are many files in Murasaki's output. Which are essential for GMV? †

GMV requires these files:

.seqs
.anchors
sequence files (.fa, .gbk, etc.)

GMV optionally (and automatically, if exists) reads these files:

.anchors.details
.stats.tfidf
.repeats
sequence length files: (.fa.length, .gbk.length, etc.)
.ntseqs (tmurasakix generates this)

and GMV may generate:

.stats.tfidf (if this doesn't exist but .anchors.details is available)
detailed sequence length files: (.fa.len, .gbk.len, etc.)
.bmk (bookmark)

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Platform specific FAQ †

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MacOS X †

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Is Snow Leopard supported? †

Surely. I'm writing the code on Snow Leopard.

The binary distribution works on MacOS X 10.4 (Tiger) and later (PPC and Intel platforms are supported). It works with Quartz (the native graphics interface of MacOS X), but It'll be easy to comple with X11 if you try to compile by yourself.

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I'm running Panther (or older) MacOS X! †

You can compile/run GMV, if you have X11 and GTK+ installed on your Mac. But this may need some hacking effort today, because MacPorts? no longer supports older versions than Tiger.

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Microsoft Windows †

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Which version of Windows are supported? †

GMV works on Windows 2000, XP and Vista.

Running the binary requires GTK+ runtime. It is also possible to build on Cygwin or MinGW/MSYS. The distributed GMV binary is cross-compiled on my Mac with MinGW library.

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