Best Visualization Apis For Conserved Gene Clusters
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10.1 years ago
skonietz ▴ 30

Hello!

I have a couple of lists of neighboring genes from several genomes. The data reflect conserved neighborhoods, however, not all genes are conserved. I would like to display the single gene clusters in an overview picture (without the need of automatically mapping corresponding genes to each other). It is just about visualizing the genome names and the genes as arrows. But the whole process should support automation!

One additional requirement considering the output format is that I still need to modify the coloring after the image has been rendered. Also, it should be possible to attach labels to the genes (= free text) as post processing. Some vector format should be fine.

Each gene comes with its coordinates and its direction (+/-). I don't need homology search.

I would like to automate the generation of images that visualize the conserved neighborhoods.

The result should look like this:

Genome 1 ----------|||||||||||||||| >----------||||||||||| > ------------- < ||||||||||||||| ----------

Genome 2 -----|||||||||||||||| >----------||||||||||| > ------------- < ||||||||||||||| ---------------

Genome 3 ----------|||||||||||||||| >---||||||||||| > -------------------- < ||||||||||||||| ----------

...

...

Genome N ----------|||||||||||||||| >----------||||||||||| > ------------- < ||||||||||||||| ----------

Of course, I could start programming this myself, but it would be nice if it already exists as freeware.

Can anyone help me? Best regards Sebastian

gene • 3.8k views
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10.1 years ago
ff.cc.cc ★ 1.3k

Have a look at genometools here

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10.1 years ago

You can have a look at the GMOD web site for comparative genomics tools:

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Dear Sir

I am trying to make synteny analysis on e.coli and mycobacteria with its entire strains. I downloaded data from NCBI Ftp site. some organism having multiple genome but in one genome it is having thousands of genes listed separately. As a new student to this field I don't know make MSA with two organisms which having more than one genome and each genome carrying separate genes inside it. Final results should be in .aln format. Please help me a way out

Regards

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10.1 years ago
skonietz ▴ 30

Looks quite good, though I am not an expert in C programming.

Does something similar exist for Java?

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This project is hosted in sourceforge, but I never tried it: http://sourceforge.net/projects/gdvtk/ See Bioinformatics, 2004 Mar 22;20(5):727-34. Java-based application framework for visualization of gene regulatory region annotations

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