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Checking and editing contigs the new way

The next important component in our strategy is the "Next Problem" function in the Contig Editor (see section Next problem). This function moves the cursor to the next position in the consensus where there is a "problem". A problem is found by applying the consensus calculation (in either of the two modes described above) to the contig. The cursor alights on the first dash ("-") or padding character ("*") found to the right of the current location. To edit a contig the user selects "find next problem" repeatedly, knowing that it will ignore poor quality data, and only move to places where there is a conflict between good data (although see later where we point out that other new problems are likely to be discovered). The time consuming impact of the poor quality data is reduced in two ways: first by being ignored altogether if below the threshold, and secondly because, even for the data above the threshold, the poorer the data the less it contributes to the outcome of the consensus calculation.


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This page is maintained by James Bonfield. Last generated on 29 April 1996.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_6.html