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Do I have to use exons as seeds or can I align with the whole sequence?

April 26, 2017align exons seeds sequence

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Do I have to use exons as seeds or can I align with the whole sequence?

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No, you do not have to supply an exon candidate file. However, if you do not supply one, the program will align the entire sequence with the search database, which can take an extremely long time. If you do not supply an exon file, you should make absolutely certain that you are submitting a repeat-masked sequence. Submitting an unrepeat-masked sequence with no exon file to the alignment program will result in an explosion of hits.