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Editing can take up a significant portion of the time taken to finish a sequencing project. Gap4 has a selection of searches (see section Searching) designed to speed up this process. The problems that require most attention are conflicts between good bases. Where base confidence values are present it should be unnecessary to edit all conflicting bases as, in general, this will amount to adjusting poor quality data to agree with good quality data, in which case the consensus sequence should be correct anyway.

Pads in the consensus should not be considered a problem requiring edits because it is possible to output the consensus sequence (from the main Gap4 File menu) with pads stripped out. Obviously poorly defined pads (a mixture of several pads and real bases) require checking in the same manner as other poorly defined consensus bases.

If you wish to check all base conflicts set the consensus algorithm to Frequency (see section The Consensus Algorithms) and the consensus cutoff to 100. The consensus will then be a dash in all places where there is not a 100% agreement in the sequences. The "Next Problem" editor button will then step one at a time through each conflict.

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This page is maintained by staden-package. Last generated on 22 October 2002.