Lee Byungwook, Hong Taehui, Byun Sang Jin, Woo Taeha, Choi Yoon Jeong
Korean BioInformation Center, KRIBB, Daejeon 305-817, Korea.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W159-62. doi: 10.1093/nar/gkm369. Epub 2007 May 25.
We present a web-based server, called ESTpass, for processing and annotating sequence data from expressed sequence tag (EST) projects. ESTpass accepts a FASTA-formatted EST file and its quality file as inputs, and it then executes a back-end EST analysis pipeline consisting of three consecutive steps. The first is cleansing the input EST sequences. The second is clustering and assembling the cleansed EST sequences using d2_cluster and CAP3 programs and producing putative transcripts. From the CAP3 output, ESTpass detects chimeric EST sequences which are confirmed through comparison with the nr database. The last step is annotating the putative transcript sequences using RefSeq, InterPro, GO and KEGG gene databases according to user-specified options. The major advantages of ESTpass are the integration of cleansing and annotating processes, rigorous chimeric EST detection, exhaustive annotation, and email reporting to inform the user about the progress and to send the analysis results. The ESTpass results include three reports (summary, cleansing and annotation) and download function, as well as graphic statistics. They can be retrieved and downloaded using a standard web browser. The server is available at http://estpass.kobic.re.kr/.
我们展示了一个名为ESTpass的基于网络的服务器，用于处理和注释来自表达序列标签（EST）项目的序列数据。ESTpass接受一个FASTA格式的EST文件及其质量文件作为输入，然后执行一个由三个连续步骤组成的后端EST分析流程。第一步是清理输入的EST序列。第二步是使用d2_cluster和CAP3程序对清理后的EST序列进行聚类和组装，并生成推定转录本。从CAP3输出中，ESTpass检测嵌合EST序列，并通过与nr数据库比较进行确认。最后一步是根据用户指定的选项，使用RefSeq、InterPro、GO和KEGG基因数据库对推定转录本序列进行注释。ESTpass的主要优点是整合了清理和注释过程、严格的嵌合EST检测、详尽的注释以及通过电子邮件报告来告知用户进展情况并发送分析结果。ESTpass的结果包括三份报告（总结、清理和注释）以及下载功能，还有图形统计。它们可以使用标准网页浏览器进行检索和下载。该服务器可在http://estpass.kobic.re.kr/获取。
