How can we find non-coding expressed sequence on whole genome sequences data? should I do the blastn?
Please take a moment to review your question again, provide us with a more compreshensive explaination of what you are trying to do and what kind of data you are dealing with. Also try to understand the question and your experimental setting yourself first, e.g. you most likely mean transcribed not 'expressed' which implies coding. If your question is really important to you you should take that time, otherwise it is maybe not relevant.
What do you mean "annotate" ? do you want a term from a controlled vocabulary ?
Blastx transcripts from for example RNA-seq against protein database. Once that don't have a hit are either unknown or non-coding.
Be careful, you most likely cannot answer such a vague question correctly.
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