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RSAT 2022：调控序列分析工具。

RSAT 2022: regulatory sequence analysis tools.

机构信息

Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France.

Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.

出版信息

Nucleic Acids Res. 2022 Jul 5;50(W1):W670-W676. doi: 10.1093/nar/gkac312.

DOI:10.1093/nar/gkac312
PMID:35544234
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9252783/
Abstract

RSAT (Regulatory Sequence Analysis Tools) enables the detection and the analysis of cis-regulatory elements in genomic sequences. This software suite performs (i) de novo motif discovery (including from genome-wide datasets like ChIP-seq/ATAC-seq) (ii) genomic sequences scanning with known motifs, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations and (v) comparative genomics. RSAT comprises 50 tools. Six public Web servers (including a teaching server) are offered to meet the needs of different biological communities. RSAT philosophy and originality are: (i) a multi-modal access depending on the user needs, through web forms, command-line for local installation and programmatic web services, (ii) a support for virtually any genome (animals, bacteria, plants, totalizing over 10 000 genomes directly accessible). Since the 2018 NAR Web Software Issue, we have developed a large REST API, extended the support for additional genomes and external motif collections, enhanced some tools and Web forms, and developed a novel tool that builds or refine gene regulatory networks using motif scanning (network-interactions). The RSAT website provides extensive documentation, tutorials and published protocols. RSAT code is under open-source license and now hosted in GitHub. RSAT is available at http://www.rsat.eu/.

摘要

RSAT（调控序列分析工具）可用于检测和分析基因组序列中的顺式调控元件。该软件套件可执行以下操作：(i)从头 motif 发现（包括来自 ChIP-seq/ATAC-seq 等全基因组数据集）；(ii)用已知 motif 扫描基因组序列；(iii) motif 分析（质量评估、比较和聚类）；(iv)调控变异分析；(v)比较基因组学。RSAT 包含 50 个工具。提供了 6 个公共 Web 服务器（包括一个教学服务器），以满足不同生物社区的需求。RSAT 的理念和创新之处在于：(i)根据用户需求提供多模式访问，通过 Web 表单、本地安装的命令行和可编程的 Web 服务；(ii)支持几乎任何基因组（动物、细菌、植物，总计超过 10000 个可直接访问的基因组）。自 2018 年 NAR Web 软件专刊以来，我们开发了一个大型的 REST API，扩展了对其他基因组和外部 motif 集合的支持，增强了一些工具和 Web 表单，并开发了一种新的工具，该工具使用 motif 扫描（网络交互）构建或细化基因调控网络。RSAT 网站提供了广泛的文档、教程和已发表的方案。RSAT 代码采用开源许可证，现托管在 GitHub 上。RSAT 可在 http://www.rsat.eu/ 上获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/73e5/9252783/0221ec70b82f/gkac312fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/73e5/9252783/3772fe83f13f/gkac312figgra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/73e5/9252783/aa262b170fe4/gkac312fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/73e5/9252783/0221ec70b82f/gkac312fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/73e5/9252783/3772fe83f13f/gkac312figgra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/73e5/9252783/aa262b170fe4/gkac312fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/73e5/9252783/0221ec70b82f/gkac312fig2.jpg

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