title: HMMCAS: A Web Tool for the Identification and Domain Annotations of CAS Proteins.
abstract: 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.
authors.forename: Guoshi
authors.initials: G
authors.lastname: Chai
authors.forename: Min
authors.initials: M
authors.lastname: Yu
authors.forename: Lixu
authors.initials: L
authors.lastname: Jiang
authors.forename: Yaocong
authors.initials: Y
authors.lastname: Duan
authors.forename: Jian
authors.initials: J
authors.lastname: Huang
mesh_terms: D061271:Acidobacteria / Q000235:genetics; D000465:Algorithms; D001105:Archaea / Q000235:genetics; D019843:Archaeal Proteins / Q000737:chemistry; D001419:Bacteria / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry; D064113:CRISPR-Cas Systems; D019295:Computational Biology / Q000379:methods*; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D020407:Internet; D008390:Markov Chains; D063747:Methanocaldococcus / Q000235:genetics; D056686:Mimiviridae / Q000235:genetics; D009876:Operon; D010802:Phylogeny; D000072417:Protein Domains; D020543:Proteome; D040901:Proteomics; D012984:Software
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D020543:Proteome