QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects
QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects
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DOI：
10.1093/bioinformatics/btp670
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发表时间：
2010-02-01
期刊：
影响因子：
5.8
通讯作者：
Martin, Jean-Francois
中科院分区：
文献类型：
--
作者：
Meglecz, Emese;Costedoat, Caroline;Martin, Jean-Francois
QDD是一个开放获取的程序，提供了一个用户友好的工具，用于从大量的DNA序列中进行微卫星检测和引物设计。该程序被设计为处理从富集的DNA文库的焦磷酸测序获得的原始序列的处理的所有步骤，但它也适用于通过其他测序方法获得的数据，使用FASTA文件作为输入。QDD完成以下任务：标签分选，接头/载体去除，消除冗余序列，检测可能的基因组多拷贝（重复的基因座或转座元件），严格选择目标微卫星和可定制的引物设计。它可以在标签分选步骤中处理多达一百万个几百个碱基对的序列，并且在单个输入中处理多达50000个序列。对于涉及序列相似性估计的步骤，参见下文。
QDD is an open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences. The program is designed to deal with all steps of treatment of raw sequences obtained from pyrosequencing of enriched DNA libraries, but it is also applicable to data obtained through other sequencing methods, using FASTA files as input. The following tasks are completed by QDD: tag sorting, adapter/vector removal, elimination of redundant sequences, detection of possible genomic multicopies (duplicated loci or transposable elements), stringent selection of target microsatellites and customizable primer design. It can treat up to one million sequences of a few hundred base pairs in the tag-sorting step, and up to 50 000 sequences in a single input. le for the steps involving estimation of sequence similarity.