The RDP (Ribosomal Database Project) continues.

NUCLEIC ACIDS RESEARCH, no. 1.0 (2000): 173-174

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摘要

The Ribosomal Database Project (RDP-II), previously described by Maidak et al,, continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 7.1 (September 17, 1999) included more than 10 700 small subunit rRNa sequences. More than 850 type strain sequences were identified and ...更多

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简介
  • C rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment length polymorphism (T-RFLP) experiments.
  • 10 700 small subunit (SSU) rRNA sequences in aligned form and more than 21 000 sequences in unaligned form.
  • Phylogenetic trees continue to be available for the sequences in the rRNA alignments.
  • They have been assembled by sequential addition of new sequences onto subtrees drawn from the previous trees, using a maximum-likelihood approach
  • RDP-II serves as a repository for published alignments and masks used in trees.
  • Extracting these alignments and masks will support recalculation of published rRNA phylogenetic trees.
重点内容
  • C rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment length polymorphism (T-RFLP) experiments
  • Phylogenetic trees continue to be available for the sequences in the rRNA alignments
  • They have been assembled by sequential addition of new sequences onto subtrees drawn from our previous trees, using a maximum-likelihood approach
  • RDP-II serves as a repository for published alignments and masks used in trees
  • A brief description of each analysis command available on the WWW server is listed in Table 1
  • The RDP-II data and analysis services can be found at http://
结果
  • These data are available for download from the RDP-II WWW and anonymous ftp servers.
  • Two new analysis commands have been added: Sequence
  • A brief description of each analysis command available on the WWW server is listed in Table 1.
  • Programs and services were used and the method of access.
  • The RDP-II data and analysis services can be found at http://
  • Rdp.cme.msu.edu/ .
  • This new mirror site should provide better access to RDP-II for researchers in that part of the world.
  • The Illinois site remains available with an automated electronic mail server; its address is server@rdp.life.uiuc.edu .
  • To obtain an overview of what data and services are currently available,
  • Analyzes the occurrence of a specified ‘probe’ sequence in a data set.
  • Determines the most similar RDP-II sequences to a user sequence.
  • Aligns a user sequence to the most similar sequence in the RDP-II data sets.
  • Calculates a similarity/dissimilarity matrix of RDP-II and/or user sequences.
  • Extracts columns from the full RDP-II alignment, with identical neighboring sequences condensed into one sequence.
  • Allows selection of sequences from a dynamically displayed taxonomic hierarchy.
  • The selected sequences can be downloaded or included as input in other RDP-II analysis functions.
  • Uses data in the ABI sequencer format to generate a similarity matrix of lane data from T-RFLP result data.
结论
  • Performs ‘in silico’ T-RFLP experiments in the RDP data set, facilitating experiment design and analysis.
  • A Java applet that displays and manipulates the phylogenetic trees, creates subtrees, or selects sequences for inclusion as input in other
  • Electronic mail correspondence with RDP-II staff should be addressed to curator@cme.msu.edu .
  • Those without access to Email may contact the RDP-II staff via telephone (+1 517 432 4998), fax (+1 517 353 8957) or regular mail.
  • Release 8.0 will occur in 2000 and it represents an anticipated doubling of the number of rRNA sequences available in the
  • Improved user query access to RDP data is being developed.
表格
  • Table1: WWW analytical commands
Download tables as Excel
引用论文
  • Maidak,B.L., Cole,J.R., Parker,C.T.,Jr, Garrity,G.M., Larsen,N., Li,B., Lilburn,T.G., McCaughey,M.J., Olsen,G.J., Overbeek,R., Pramanik,S., Schmidt,T.M., Tiedje,J.M. and Woese,C.R. (1999) Nucleic Acids Res., 27, 171–173.
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  • Benson,D.A., Boguski,M.S., Lipman,D.J., Ostell,J., Ouellette,B.F., Rapp,B.A. and Wheeler,D.L. (1999) Nucleic Acids Res., 27, 12–17. Updated article in this issue: Nucleic Acids Res. (2000) 28, 15–18.
    Google ScholarLocate open access versionFindings
  • Stoesser,G., Tuli,M.A., Lopez,R. and Sterk,P. (1999) Nucleic Acids Res., 27, 18–24. Updated article in this issue: Nucleic Acids Res. (2000) 28, 19–23.
    Google ScholarLocate open access versionFindings
  • Sugawara,H., Miyazaki,S., Gojobori,T. and Tateno,Y. (1999) Nucleic (2000) 28, 24–26.
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  • Felsenstein,J. (1981) J. Mol. Evol., 17, 368–376.
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  • Olsen,G.J., Matsuda,H., Hagstrom,R. and Overbeek,R. (1994) Comput. Appl. Biosci., 10, 41–48.
    Google ScholarLocate open access versionFindings
  • Gutell,R.R. (1994) Nucleic Acids Res., 22, 3502–3507.
    Google ScholarLocate open access versionFindings
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