DSAP: deep-sequencing small RNA analysis pipeline.
DSAP: deep-sequencing small RNA analysis pipeline.
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DOI：
10.1093/nar/gkq392
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发表时间：
2010-07
影响因子：
14.9
通讯作者：
Tang P
中科院分区：
文献类型：
--
作者：
Huang PJ;Liu YC;Lee CC;Lin WC;Gan RR;Lyu PC;Tang P
DSAP是一种自动化的多任务Web服务，旨在为分析由下一代测序技术生成的深度测序小RNA数据集提供整体解决方案。DSAP使用制表符分隔的文件作为输入格式，该文件保存由Solexa测序平台生成的唯一序列读取(标签)及其相应的副本数量。输入数据将在DSAP中经历四个分析步骤：(I)清理：移除接头和聚A/T/C/G/N核苷酸；(Ii)聚类：将清理后的序列标签分组为唯一的序列簇；(Iii)非编码RNA(NcRNA)匹配：与来自ncRNA数据库RFAM(http://rfam.sanger.ac.uk/)；)的转录序列文库进行序列同源性映射；和(Iv)已知miRNA匹配：基于序列同源性检测miRBase(http://www.mirbase.org/))中的已知miRNAs。与匹配的ncRNAs和miRNAs对应的表达水平在链接到外部数据库的多色可点击条形图中汇总。DSAP还能够使用log2比例的颜色矩阵显示不同工作的miRNA表达水平。此外，还提供了跨物种比较功能，以显示存放在miRBase中的已识别miRNAs在不同物种中的分布。DSAP可在http://dsap.cgu.edu.tw.上获得
DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log2-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw.
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影响因子：
14.9
作者：
Griffiths-Jones, S;Bateman, A;Eddy, SR
通讯作者：
Eddy, SR
影响因子：
14.9
作者：
Wilm, Andreas;Higgins, Desmond G.;Notredame, Cedric
通讯作者：
Notredame, Cedric
影响因子：
--
作者：
Griffiths-Jones, Sam
通讯作者：
Griffiths-Jones, Sam
影响因子：
9.5
作者：
Olson, Sue A
通讯作者：
Olson, Sue A
影响因子：
14.9
作者：
Moretti, Sebastien;Wilm, Andreas;Higgins, Desmond G.;Xenarios, Ioannis;Notredame, Cedric
通讯作者：
Notredame, Cedric