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.
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.
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.
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.
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.
The contig101 (4 clones) was end-merged to contig76 (18 clones), and contig193 (29 clones) was end-merged to contig1 (3 clones), by the "End to End" function at terminal cutoff 10-12 and match value 2. This result was referred as PhaseIA and used as standard version.
It is still unclear how to evaluate the quality of the approximate end-to-end functions in terms of exact end-to-end sum-rate maximization.
The application layer comprises the end-to-end protocols that are required to implement the end-to-end functions, and some well-known protocols sitting on it include HTTP, SMTP, POP3, IMAP4, TELNET, FTP, and DNS.
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].
