Mouse BAC ends quality assessment and sequence analyses.
Mouse BAC ends quality assessment and sequence analyses.
复制标题
小鼠 BAC 结束质量评估和序列分析。
DOI：
10.1101/gr.179201
复制
发表时间：
2001
期刊：
影响因子：
7
通讯作者：
Fraser,CM
中科院分区：
文献类型：
--
作者：
Zhao,S;Shatsman,S;Ayodeji,B;Geer,K;Tsegaye,G;Krol,M;Gebregeorgis,E;Shvartsbeyn,A;Russell,D;Overton,L;Jiang,L;Dimitrov,G;Tran,K;Shetty,J;Malek,JA;Feldblyum,T;Nierman,WC;Fraser,CM
基因组研究所（TIGR）的一个大规模BAC末端测序项目已经产生了迄今为止最广泛的小鼠基因组序列标记集之一。测序成功率> 80%，平均读取长度为485 bp，使用ABI 3700毛细管测序仪，我们从来自文库RPCI-23和RPCI-24的257，318个克隆中生成了449，234个非冗余小鼠BAC末端序列（mBES），总计218 Mb，代表15×克隆覆盖率，7%序列覆盖率，在整个基因组中每隔7 kb有一个标记。共有191，916个BAC具有来自两端的序列，提供12×基因组覆盖率。Q20平均长度为406 bp，84%的碱基质量分数≥ 20。RPCI-24 mBES平均比RPCI-23序列具有更多的Q20碱基和更长的读段。ABI 3700测序仪和样品跟踪系统确保> 95%的mBES与正确的克隆标识符相关联。我们已经发现相当一部分mBES含有L1重复序列，并且大约48%的克隆具有≥ 100 bp连续独特Q20碱基的两端。约3%的mBES与EST匹配，小鼠与人或大鼠之间> 70%的匹配是保守的。大约0.1%的mBES含有STS。约0.2%的mBES匹配人类完成的序列，并且这些序列中> 70%具有EST命中。分析表明，我们的高质量的小鼠BAC末端序列将是一个宝贵的资源，以社会。
A large-scale BAC end-sequencing project at The Institute for Genomic Research (TIGR) has generated one of the most extensive sets of sequence markers for the mouse genome to date. With a sequencing success rate of >80%, an average read length of 485 bp, and ABI3700 capillary sequencers, we have generated 449,234 nonredundant mouse BAC end sequences (mBESs) with 218 Mb total from 257,318 clones from libraries RPCI-23 and RPCI-24, representing 15× clone coverage, 7% sequence coverage, and a marker every 7 kb across the genome. A total of 191,916 BACs have sequences from both ends providing 12× genome coverage. The average Q20 length is 406 bp and 84% of the bases havephredquality scores ≥ 20. RPCI-24 mBESs have more Q20 bases and longer reads on average than RPCI-23 sequences. ABI3700 sequencers and the sample tracking system ensure that > 95% of mBESs are associated with the right clone identifiers. We have found that a significant fraction of mBESs contains L1 repeats and ∼48% of the clones have both ends with ≥ 100 bp contiguous unique Q20 bases. About 3% mBESs match ESTs and > 70% of matches were conserved between the mouse and the human or the rat. Approximately 0.1% mBESs contain STSs. About 0.2% mBESs match human finished sequences and > 70% of these sequences have EST hits. The analyses indicate that our high-quality mouse BAC end sequences will be a valuable resource to the community.