Specifically, for each of the 38 species listed in Table 1, we aligned the comparative-grade finished sequence of each BAC to the corresponding human-grade finished sequence for that species using the program Cross Match [ 28].
Importantly, comparative-grade finished sequence was also available for all 541 sequenced BACs in this first data set.
Most of the BAC sequences in this second data set have not been refined to human-grade finished sequence.
The resulting alignments were manually examined and corrected when contigs in the comparative-grade finished sequence had an ambiguous endpoint and/or order in the alignment.
The total number of BACs (Total BACs) and the amount of comparative-grade finished sequence generated (Total Mb) for each species are shown.
Notably, we found an identical frequency of gaps in an earlier study that involved analyzing the comparative-grade finished sequence of 116 vertebrate BACs [ 5].
We analyzed the first data set for the presence of gaps in the comparative-grade finished sequence of the 541 BACs.
We analyzed the comparative-grade finished sequence generated for the 2,031 BACs in the second data set for the presence of captured and uncaptured gaps.
The total number of BACs (Total BACs) and the amount of comparative-grade finished sequence generated (Total Mb) for each genomic region are shown.
Our studies have shown that the quality of comparative-grade finished sequence is very high, with residual gaps and errors mostly residing within repetitive sequences [ 5].
From the final alignments, we then catalogued the location, size, and sequence composition of all gaps in the comparative-grade finished sequence; further, the number of shotgun-library subclones spanning each gap (as detected by establishing the locations of all sequence reads in the human-grade finished sequence) was also determined.
