CAP3: A DNA sequence assembly program
CAP3: A DNA sequence assembly program
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DOI：
10.1101/gr.9.9.868
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发表时间：
1999-09-01
期刊：
影响因子：
7
通讯作者：
Madan, A
中科院分区：
文献类型：
--
作者：
Huang, XQ;Madan, A
我们描述了第三代CAP序列组装程序。CAP 3程序包括许多改进和新功能。该程序具有剪切5'和3'低质量读段区域的能力。它使用碱基质量值来计算读段之间的重叠、构建读段的多序列比对以及生成共有序列。该程序还使用正向-反向约束来纠正组装错误和连接重叠群。CAP 3在四个BAC数据集上的结果。CAP 3的性能进行了比较与PHRAP的BAC数据集的数量。PHRAP通常比CAP 3产生更长的重叠群，而CAP 3通常比PHRAP在共有序列中产生更少的错误。在具有Forward-reverse约束的低通数据上，使用CAP 3比使用PHRAP更容易构建支架。
We describe the third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new Features. The program has a capability to clip 5' and 3' low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward-reverse constraints to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with Forward-reverse constraints.