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Candidate cosmids encompassing the β TCR locus were identified by screening libraries constructed from yeast artificial chromosome (YAC) DNA or total genomic DNA with probes prepared from V gene segments, β locus-specific sequence-tagged sites, or human repetitive DNA (for cosmids derived from YACs). These cosmids were derived from the DNA of six different individuals (libranes), representing 12 possible distinct haplotypes. A physical map of 139 cosmid clones was constructed by a combination of Southern (DNA) blot hybridization, restriction digest analysis, and alignment of DNA sequence from the ends of cosmid inserts with completed sequence contigs (33). This cosmid array represents a sevenfold average coverage of the locus. The complete DNA sequence of the locus was obtained by applying a high-redundancy (eightfold coverage) shotgun method to 23 cosmids (47) and a primer-walking directed method to three cosmids (8). The sequence and its annotation are deposited in the Genome Sequence Data Base (accession numbers L36092, L36190, and U03115). On the basis of resequencing >60 kb of DNA, we estimate that the sequence contains, on average, one error per 5 kb. For specific details of the sequencing strategy (including chemistry, assembly of repeats, and precision estimates), see (47).
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20
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Non-TCR genes were identified by Xgrail (version 1.2) and BlastX. Similarity analyses were performed with the Smith-Waterman comparison algorithm on a Masspar Supercomputer (MpSRCH; Intelligenetics), with the Inherit analysis program (Applied Biosystems), or with cross_match (4).
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We thank A Smit for extensive analysis of genomewide interspersed repeats in this sequence; P. Green for cross_match, a sequence comparison program; X. Huang for his multiple sequence alignment program (MAP); D. Gordon and T. Smith for computer scripts; K Cattell for the MpSRCH analysis, Applied Biosystems and Masspar for allowing us to use early test software; technicians at the California Institute of Technology and the University of Washington for performing the DNA sequencing; P. Charmley for helpful discussion; and M. E. Aheam for technical assistance. B.F.K. thanks Canadian Genome Analysis and Technology and the Natural Sciences and Engineering Research Council of Canada for their support. Supported by grants from the Department of Energy and NIH.
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