RCDI/eRCDI: A web-server to estimate codon usage deoptimization

被引：54
|
作者：
Puigbò P. [1 ]
Aragonès L. [2 ]
Garcia-Vallvé S. [3 ]
机构：
[1] National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
[2] Department of Microbiology, University of Barcelona
[3] Department of Biochemistry and Biotechnology, Nutrigenomics Research Group, Rovira i Virgili University
来源：
BMC Research Notes | / 3卷 / 1期
基金：
美国国家卫生研究院;
关键词：
Codon; Reference Genome; Amino Acid Composition; Codon Usage; Test Sequence;
D O I：
10.1186/1756-0500-3-87
中图分类号：
学科分类号：
摘要：
Background. The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome. Findings. RCDI/eRCDI is a web application server that calculates the Relative Codon Deoptimization Index and a new expected value for the RCDI (eRCDI). The RCDI is used to estimate the similarity of the codon frequencies of a specific gene in comparison to a given reference genome. The eRCDI is determined by generating random sequences with similar G+C and amino acid composition to the input sequences and may be used as an indicator of the significance of the RCDI values. RCDI/eRCDI is freely available at http://genomes.urv.cat/CAIcal/RCDI. Conclusions. This web server will be a useful tool for genome analysis, to understand host-virus phylogenetic relationships or to infer the potential host range of a virus and its replication strategy, as well as in experimental virology to ease the step of gene design for heterologous protein expression. © 2010 Puigb et al; licensee BioMed Central Ltd.
引用
收藏
相关论文
共 50 条
  • [41] Epitopia: a web-server for predicting B-cell epitopes
    Nimrod D Rubinstein
    Itay Mayrose
    Eric Martz
    Tal Pupko
    BMC Bioinformatics, 10
  • [42] Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region
    Burns, CC
    Shaw, J
    Campagnoli, R
    Jorba, J
    Vincent, A
    Quay, J
    Kew, O
    JOURNAL OF VIROLOGY, 2006, 80 (07) : 3259 - 3272
  • [43] ACDtool: a web-server for the generic analysis of large data sets of counts
    Claverie, Jean-Michel
    Thi Ngan Ta
    BIOINFORMATICS, 2019, 35 (01) : 170 - 171
  • [44] Analysis of task assignment policies in scalable distributed web-server systems
    Colajanni, M
    Yu, PS
    Dias, DM
    IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 1998, 9 (06) : 585 - 600
  • [45] DNS-based load balancing in distributed Web-server systems
    Hong, Y. S.
    No, J. H.
    Kim, S. Y.
    FOURTH IEEE WORKSHOP ON SOFTWARE TECHNOLOGIES FOR FUTURE EMBEDDED AND UBIQUITOUS SYSTEMS AND THE SECOND INTERNATIONAL WORKSHOP ON COLLABORATIVE COMPUTING, INTEGRATION, AND ASSURANCE, PROCEEDINGS, 2006, : 251 - +
  • [46] SIRES: A WEB-SERVER TOOL FOR SEARCHING OF IRON-RESPONSIVE ELEMENTS
    Sanchez, M.
    Campillos, M.
    Cases, I.
    Frigola-Quintana, G.
    Hentze, M.
    HAEMATOLOGICA-THE HEMATOLOGY JOURNAL, 2010, 95 : 424 - 424
  • [47] STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
    Snel, B
    Lehmann, G
    Bork, P
    Huynen, MA
    NUCLEIC ACIDS RESEARCH, 2000, 28 (18) : 3442 - 3444
  • [48] ECG Monitoring System Using ARM9 Web-Server
    Kumari, L. V. Rajani
    Sai, Y. Padma
    Balaji, N.
    Kumar, K. Tejaswi
    2015 GLOBAL CONFERENCE ON COMMUNICATION TECHNOLOGIES (GCCT), 2015, : 234 - 237
  • [49] Placement of Web-server proxies with consideration of read and update operations on the Internet
    Jia, XH
    Li, DY
    Hu, XD
    Wu, WL
    Du, DZ
    COMPUTER JOURNAL, 2003, 46 (04): : 378 - 390
  • [50] Levels of Presenting Ontologies, Languages, Mathematical Models, and Ontology Web-Server Project in Web 2.0
    Beniaminov, E. M.
    Lapshin, V. A.
    AUTOMATIC DOCUMENTATION AND MATHEMATICAL LINGUISTICS, 2012, 46 (02) : 59 - 67
12345