What software do you recommend for illustrating genes along a genome? The software should be free to academics, and have a simple text/tab input format. I have a list of genes, start/stop coordinates, orientation, gene function.
Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence.
It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.
Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence.
It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.
I have used circos for making some pretty cool circular plots before, but I found it a little difficult to use. YMMV
http://circos.ca/
Geneious (http://www.geneious.com/) it's commercial, but you can ask for a free trial for quick stuff. It supports many input types and can generate great graphics.
As Sajjad says I would recommend Artemis for smaller visualisation..IGV is also useful for this. Circos is quite difficult in setup and adjustments but very good for visualisation.
CGview is a good tool for showing genes with annotation on genomes. GenoPlotR package can also be useful.
As mentioned above
Artemis is way to go.
http://www.sanger.ac.uk/science/tools/artemis
I always want to try Circos, it looks so cool, yet
it is difficult to format our data in order to fit into their criteria, etc.
GBrowse is better. It works flawlessly and they have a good email list for support. I have used it for 3 genomes so far without any issues.
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