Annotation of sequence obtained from illumina hiseq

[anishashajan]

Have received sequence file of large genome obtained from illumina hiseq.Which software would be preferred for carrying out sequence annotation?

[dpryan]

By annotate, you likely mean "align". There are a LOT of options (the linked wikipedia article is not likely to be exhaustive). The best one will likely depend on your goals and available computational resources.

[mcnelson.phd]

I think he actually might mean annotate, as in finding and calling structural motifs and functional genes.

Since you said a large genome, I'm going to assume eukaryotic. There are a number of software packages that can help you do annotation, but I've never used any of them so I'll let someone else comment on which to try first.

To get started you can always begin ORF calling with Glimmer3 and finding your tRNAs with tRNAscan.

You might also want to try posting this in the Bioinformatics forum as this one is more about handling the instruments and sequencing and not the later processing as much.

[GenoMax]

Have received sequence file of large genome obtained from illumina hiseq.Which software would be preferred for carrying out sequence annotation?

If you have a "raw" sequence file that requires alignment/assembly, then refer to dpryan's post above.

Following only applies if you have a "final" sequence file (your original post is not clear on this point) that requires annotation.

If the genome is prokaryotic then you may want to take advantage of the automatic bacterial genome annotation pipeline provided by NCBI: http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline

If this is a eukaryotic genome then this page provides a guide for the process of annotation: http://www.ncbi.nlm.nih.gov/genome/a...n_euk/process/

[dpryan]

I think he actually might mean annotate, as in finding and calling structural motifs and functional genes.

Could be, "annotate" is an incredibly overused word in bioinformatics, such that I think many people don't know that it requires an object (i.e., annotate it with what?). It's like asking a molecular biologist how to "measure a protein sample"

[mcnelson.phd]

Could be, "annotate" is an incredibly overused word in bioinformatics, such that I think many people don't know that it requires an object (i.e., annotate it with what?). It's like asking a molecular biologist how to "measure a protein sample"

True. I've had a number of people ask me how to annotate their raw read data w/o realizing they first need to assemble it so it doesn't hurt to make sure the OP is asking the right questions so they can get the right answers.

[anishashajan]

Thanks dpryan, mcnelson.phd & genomax for the suggestions.I have the fasta file of a sample obtained from illumina hiseq genome analyser.Want to do complete annotation of the file and should include the number of chromosomes,unplaced regions,coding and non coding etc. How is Nextgene software can it be used to get the complete annotation of the sample file?