Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl
Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl
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DOI：
10.1093/bioinformatics/btp519
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发表时间：
2009-10-15
期刊：
影响因子：
5.8
通讯作者：
van Helden, Jacques
中科院分区：
文献类型：
--
作者：
Sand, Olivier;Thomas-Chollier, Morgane;van Helden, Jacques
合适的序列数据集的准备是所有基因组分析的起点。我们目前检索ensembl-seq，一个应用程序，大大简化了检索的序列从Ensembl数据库，通过我们的用户友好的网站或Web服务。用户提供Ensembl标识符或基因名称，程序返回相应的上游、下游、内含子、外显子、UTR或整个基因序列。retrieve-ensembl-seq还提供了一种多生物体模式，以从任何分类学水平的同源基因中检索序列。我们介绍了各种原始的过滤器，如编码片段的掩蔽和避免序列冗余的基因与多个转录本。retrieve-ensembl-seq包含在软件套件调节序列分析工具（RSAT）中，允许将检索到的序列即时提交给进一步的分析工具。
The preparation of an appropriate sequence dataset is the starting point of all genomic analyses. We present retrieve-ensembl-seq, an application that considerably eases the retrieval of sequences from the Ensembl database, via our user-friendly web site or web services. The user provides Ensembl identifiers or gene names, and the program returns corresponding upstream, downstream, intronic, exonic, UTR or whole gene sequences. retrieve-ensembl-seq also offers a multiple organism mode to retrieve sequences from homologous genes at any taxonomical level. And we introduce various original filters such as the masking of coding fragments and the avoidance of sequence redundancy for genes with multiple transcripts. retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools.