HMMCAS: A Web Tool for the Identification and Domain Annotations of CAS Proteins
HMMCAS: A Web Tool for the Identification and Domain Annotations of CAS Proteins
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HMMCAS：用于 Cas 蛋白识别和域注释的网络工具
DOI：
10.1109/tcbb.2017.2665542
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发表时间：
2019-07-01
影响因子：
4.5
通讯作者：
Huang, Jian
中科院分区：
文献类型：
--
作者：
Chai, Guoshi;Yu, Min;Huang, Jian
CRISPR-Cas（clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins）适应性免疫系统在许多细菌和大多数古细菌中被发现。这些系统由cas（CRISPR相关）操纵子编码，这些操纵子具有极其多样化的结构。描述cas操纵子组成的最关键步骤是鉴定cas基因或Cas蛋白。随着新测序的古细菌和细菌基因组的不断增加，识别新的Cas蛋白成为可能，这不仅为新的基因组编辑工具提供了候选者，而且有助于更好地了解原核免疫系统。在这里，我们描述了HMMCAS，这是一种用于检测蛋白质序列中CRISPR相关结构域和功能域的Web服务。HMMCAS使用HMMER3.1中的hmmscan相似性搜索算法，基于Cas蛋白质家族的隐马尔可夫模型的全面集合提供快速，交互式服务。它可以准确地鉴定Cas蛋白，包括那些融合蛋白，例如嗜热绿酸杆菌B（Ca B. thermophilum B）。HMMCAS还可以发现推定的cas操纵子并确定其属于哪种类型。HMMCAS可在http://i.uestc.edu.cn/hmmcas上免费获得。
The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) adaptive immune systems are discovered in many bacteria and most archaea. These systems are encoded by cas (CRISPR-associated) operons that have an extremely diverse architecture. The most crucial step in the depiction of cas operons composition is the identification of cas genes or Cas proteins. With the continuous increase of the newly sequenced archaeal and bacterial genomes, the recognition of new Cas proteins is becoming possible, which not only provides candidates for novel genome editing tools but also helps to understand the prokaryotic immune system better. Here, we describe HMMCAS, a web service for the detection of CRISPR-associated structural and functional domains in protein sequences. HMMCAS uses hmmscan similarity search algorithm in HMMER3.1 to provide a fast, interactive service based on a comprehensive collection of hidden Markov models of Cas protein family. It can accurately identify the Cas proteins including those fusion proteins, for example the Cas1-Cas4 fusion protein in Candidatus Chloracidobacterium thermophilum B (Cab. thermophilum B). HMMCAS can also find putative cas operon and determine which type it belongs to. HMMCAS is freely available at http://i.uestc.edu.cn/hmmcas.