I need some bioinformatics advice. I have two sets of seven DNA sequencing results from PCR fragments cloned into pGEM-T plasmid. Because the PCR amplicons can be incorporated into the plasmid in either of two directions, I've no way of knowing which are forward and which are reverse without trying to align each one individually in MegAlign (software from the pretty crappy suite available to me). There must be a quicker way to check alignments in both directions automatically though, right?
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Basic DNA sequence alignment problem
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