I am using wormbase to retrieve files for my project. It has an annotations.gff2 file. I need to open it in a software that can show me the scafolds and contigs in it. Can anyone please suggest to me a computational software for the same?
We are using Lasergene from DNAstar. The cost is reasonable and I think it may be useful for your needs. Check it out - just google Lasergene Genomics Suite. Not sure if we can put urls in these posts
Good success with your projects
There are several free alternatives (http://en.wikipedia.org/wiki/Genome_browser), but I think that the most used ones are:
+IGV (Integrative Genomic Viewer): http://www.broadinstitute.org/igv/
Easy to install, run in any OS. Suports other files such as bam files (for mapping reads). Great tool. Highly recommended.
+Tablet http://bioinf.scri.ac.uk/tablet/index.shtml
Easy to install, run in any OS. Fast. It is more sequence map oriented than IGV than genome annotation, but still can be useful to search specific regions associated with specific genes.
+ UCSC Genomic Browser (http://genome.ucsc.edu/), GBrowse (http://gmod.org/wiki/GBrowse) and JBrowser (http://jbrowse.org/) are genomics browser, perhaps more difficult to install, but they can be configured to be used through a server. They are commonly used in genome databases such as Flybase, TAIR or SGN. They are difficult to install if you don't have any Linux/Perl experience.
Check this out! Might be useful: Argo Genome Browser is a (free!) Java application, allows display of sequence and annotation tracks (from FASTA, Genbank, GFF, BLAST, BED, Wiggle (WIG), and Genscan files):
http://www.broadinstitute.org/annotation/argo/
Thank you everyone for the advice. I will definitely look into those.
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