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The remaining contigs were end-merged by "End to End" function and then singletons were added to the end of contigs by "Singles to End" function (cutoff of 1e-21).
Using "End to End" function at terminal cutoff 10-08 and match value 1, we merged another 74 contigs.
Then, to identify potential junctions between contigs, the entire fingerprint database was searched for matches to terminal clone fingerprints of every contig using the end to end function of FPC with cutoff values ranging from 1e-20 to 1e-07.
Finally, 2,715 contigs were end-merged by "End to End" function, and 8,077 singletons were added to the end of contigs by "keyset to FPC" function at nine successively higher cutoffs from 1e-60 to 1e-15.
Third, the remaining contigs were end-merged by "End to End" function and then singletons were added to the end of contigs by "Singles to End" function at 6 successively lower cutoffs, starting at 1e-40 and terminating at 1e-15.
2 The percentage of Q clones to total clones 2290. 3 The percentage of single clones to total clones 2290. 4 The cutoff value of 10-15 was chosen, then contig101was end-merged to contig76, and contig193 was end-merged to contig1 by "End to End" function at cutoff 10-12, respectively.
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The significant differences in assembly could be explained by the use of BAC clones that are on average approximately 25% longer in this study, by the use of EcoR1 partial digestion for BAC library production that may clone regions of the genome that are more representative and more easily assembled, and by the use of more stringent criteria for the "end-to-end" function in this study.
The Singles-to-Ends function and the Ends-to-Ends function were run at a final cutoff of 1 e-50 using automatic merges to join singletons to contig ends and contigs to contigs, respectively.
At the end, the contigs were improved using the "End to End" automerge function.
The "End to End" FPC function was then repeatedly employed to merge contigs with successively less stringent Sulston score cutoff values [ 24, 25, 28].
The resulting contigs were end-merged using the 'End to End' function, setting the 'FromEnd' parameter to 50, 'Match' to 2 and the cutoff value to 1e-40.
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