Can soemone advise on the use of Genemark output?

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Muhammad Sufian

Share the output file generated from GeneMark.

Vishal Desai

Here is my file, I have not decided my pipeline yet so may be u could help.

I think you had a long protein sequence, which you input in GeneMark, and it outputs the 'data.lst' file. Now, I think you should retrieve these sequences from this file in FASTA format, and then BLASTp them against 'nr database' to find each predicted protein's sequence homologue.

Thanks Muhammad, but I was thiking about runinng BLASTx and do u know how to perform gene ontology my mentor told me to do it.

BLASTx......but your query is already protein, so as per my thinking, BLASTp is ok.

I have no experience with GO, but following article might help you.

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003343