How can I display the orientation of sequences in a blast alignment? In particular, I am using Bl2seq to align multiple sequencing results and primers, and I would like to be able to quickly see the orientation of the aligned sequences and primers. Is there a way to do this from the BLAST website. Is there some other tool that will do this (preferably a free one)?
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If you use the NCBI Blast2sequences website, you already get the orientation together with the alignment. Above the alignments you have "Score Expect Identities Gaps Strand". The strand corresponds to the orientation: plus = forward, minus = reverse. If it reads "plus/minus" your query sequence is forward, the subject sequence reverse.
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Ok, one last try before I give up
Is the organism you are working with available at the JGI database?
Because their Blast output has arrows to indicate orientations. You will, however, be restricted to one organism (but as you mentioned primer alignment you're probably only interested in one?!)
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