Selected article for: "alignment analysis and multiple alignment analysis"
Author: Wang, Jingqiang; Ji, Jia; Ye, Jia; Zhao, Xiaoqian; Wen, Jie; Li, Wei; Hu, Jianfei; Li, Dawei; Sun, Min; Zeng, Haipan; Hu, Yongwu; Tian, Xiangjun; Tan, Xuehai; Xu, Ningzhi; Zeng, Changqing; Wang, Jian; Bi, Shengli; Yang, Huanming
Title: The Structure Analysis and Antigenicity Study of the N Protein of SARS-CoV
  • Document date: 2016_11_28
    • ID: s38k8d3l_33
    Snippet: ORF Finder (http://ww.ncbi.nlm.nih.gov/gorf/gorf.html) was used to determine ORFs, EMBOSS package (http://www.hgmp.mrc.ac.uk/Software/EMBOSS/) to characterize proteins, NetPhos (http://www.cbs.dtu.dk/services/NetPhos/) and PhosphoBase (http://www.cbs.dtu.dk/databases/PhosphoBase/) to predict phosphorylation sites, TopPred2 (http://bioweb.pasteur.fr/seqanal/interfaces/toppred.html) and ProtScale (http://us.expasy.org/cgi-bin/protscale.pl) to ident.....
    Document: ORF Finder (http://ww.ncbi.nlm.nih.gov/gorf/gorf.html) was used to determine ORFs, EMBOSS package (http://www.hgmp.mrc.ac.uk/Software/EMBOSS/) to characterize proteins, NetPhos (http://www.cbs.dtu.dk/services/NetPhos/) and PhosphoBase (http://www.cbs.dtu.dk/databases/PhosphoBase/) to predict phosphorylation sites, TopPred2 (http://bioweb.pasteur.fr/seqanal/interfaces/toppred.html) and ProtScale (http://us.expasy.org/cgi-bin/protscale.pl) to identify the hydrophobic region, ClustalW (http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/) to perform multiple-alignment and phylogenetic analysis, PSIPRED (http://bioinf.cs.ucl.ac.uk/psiform.html) to analyze secondary structures, InterproScan (http://www.ebi.ac.uk/interpro/) and CDS (Conserved Domain Search, http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) to predict conserved protein domains. All the analyses were accomplished on supercomputers DOWNING 2000/3000 (DOWNING Computers Inc., Beijing, China), SUN E10K (SUN Microsystems Inc., California, USA), SGI Origin 3800 (Silicon Graphics, Inc., California, USA), and IBM P690 (IBM Corp., New York, USA).

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