WASPS：基于网络的质粒协同性分析服务器。

WASPS: web-assisted symbolic plasmid synteny server.

机构信息

Microbiology Department, CEA, CNRS, Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette cedex 91198, France.

Département de Microbiologie, Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Paris 75015, France.

出版信息

Bioinformatics. 2020 Mar 1;36(5):1629-1631. doi: 10.1093/bioinformatics/btz745.

DOI:10.1093/bioinformatics/btz745

PMID:31589313

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7703779/

Abstract

MOTIVATION

Comparative plasmid genome analyses require complex tools, the manipulation of large numbers of sequences and constitute a daunting task for the wet bench experimentalist. Dedicated plasmid databases are sparse, only comprise bacterial plasmids and provide exclusively access to sequence similarity searches.

RESULTS

We have developed Web-Assisted Symbolic Plasmid Synteny (WASPS), a web service granting protein and DNA sequence similarity searches against a database comprising all completely sequenced natural plasmids from bacterial, archaeal and eukaryal origin. This database pre-calculates orthologous protein clustering and enables WASPS to generate fully resolved plasmid synteny maps in real time using internal and user-provided DNA sequences.

AVAILABILITY AND IMPLEMENTATION

WASPS queries befit all current browsers such as Firefox, Edge or Safari while the best functionality is achieved with Chrome. Internet Explorer is not supported. WASPS is freely accessible at https://archaea.i2bc.paris-saclay.fr/wasps/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

比较质粒基因组分析需要复杂的工具，需要处理大量的序列，这对于湿实验员来说是一项艰巨的任务。专用的质粒数据库很少，仅包含细菌质粒，并且仅提供对序列相似性搜索的访问。

结果

我们开发了 Web 辅助符号质粒同线性（WASPS），这是一项网络服务，可针对包含来自细菌、古菌和真核生物的所有完全测序的天然质粒的数据库进行蛋白质和 DNA 序列相似性搜索。该数据库预先计算了直系同源蛋白聚类，使 WASPS 能够使用内部和用户提供的 DNA 序列实时生成完全解析的质粒同线性图谱。