Genome viewer less clunky than ACT/Artemis?

[akjones]

Hello,

I'm wondering if anyone has any suggestions for a genome viewer other than ACT/Artemis? I have tried using ACT in the past but the software and layout is very clunky and I don't find it particularly useful or easy to work with. If there is a program that can read .crunch files that would be even better as I am working primarily with output from Abacas.

Thanks,

~Ana

[GenoMax]

Tablet: http://bioinf.scri.ac.uk/tablet/
IGV: http://www.broadinstitute.org/igv/
IGB: http://bioviz.org/igb/

You will have to do conversions of the .crunch files since that is not a common format.

[DNAnalyzer]

Does anyone know if there is a streamlined method for converting NCBI feature tables to GFF3 formatted features file or do I need to write something myself?

The Sequencing Ontology Project has a great definition for the GFF3 format and a link to an online validator but there is no mention of how the files are created.

http://www.sequenceontology.org/gff3.shtml

[DNAnalyzer]

I found most of what I was looking for on the NCBI ftp site. That should take care of my needs for now. What about this bit of Perl code that I ran across.

http://www.hpa-bioinformatics.org.uk/biosnippets/snippets/115

Is it the gold standard or depreciated garbage? Maybe ill give it a try.

[akjones]

Thanks, GenoMax! Do you have any suggestions about how to convert the .crunch file and what format I should convert it to? My instinct is to go straight to a fasta file, but since the output from Abacas is an alignment I am concerned about losing that information. I am pretty much a bioinformatics newbie and the file formats I have the most experience working with are fasta and fastq. If my questions seem too basic, I apologize. I am reading up on the file formats supported by tablet and the other genome viewers, hopefully that will help point me in the right direction as well.

I appreciate your help,

~Ana