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MiCA: A Web-Based Tool for the Analysis of Microbial Communities Based on Terminal-Restriction Fragment Length Polymorphisms of 16S and 18S rRNA Genes

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Abstract

A web-based resource, Microbial Community Analysis (MiCA), has been developed to facilitate studies on microbial community ecology that use analyses of terminal-restriction fragment length polymorphisms (T-RFLP) of 16S and 18S rRNA genes. MiCA provides an intuitive web interface to access two specialized programs and a specially formatted database of 16S ribosomal RNA sequences. The first program performs virtual polymerase chain reaction (PCR) amplification of rRNA genes and restriction of the amplicons using primer sequences and restriction enzymes chosen by the user. This program, in silico PCR and Restriction (ISPaR), uses a binary encoding of DNA sequences to rapidly scan large numbers of sequences in databases searching for primer annealing and restriction sites while permitting the user to specify the number of mismatches in primer sequences. ISPaR supports multiple digests with up to three enzymes. The number of base pairs between the 5′ and 3′ primers and the proximal restriction sites can be reported, printed, or exported in various formats. The second program, APLAUS, infers a plausible community structure(s) based on T-RFLP data supplied by a user. APLAUS estimates the relative abundances of populations and reports a listing of phylotypes that are consistent with the empirical data. MiCA is accessible at http://mica.ibest.uidaho.edu/.

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Acknowledgment

This research was supported by a grant from Procter and Gamble to J.A.F. and L.J.F. and by a grant from the National Institutes of Health (NIH NCRR IP20 RR16448) to L.J.F.

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Authors and Affiliations

  1. Department of Computer Science, University of Idaho, Moscow, ID, 83844, USA

    Conrad Shyu & Terry Soule

  2. Department of Biological Sciences, Life Sciences South, Rm. 252, University of Idaho, Moscow, ID 83843, USA

    Stephen J. Bent, James A. Foster & Larry J. Forney

Authors
  1. Conrad Shyu
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  2. Terry Soule
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  3. Stephen J. Bent
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  4. James A. Foster
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  5. Larry J. Forney
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Corresponding author

Correspondence to Larry J. Forney.

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Shyu, C., Soule, T., Bent, S.J. et al. MiCA: A Web-Based Tool for the Analysis of Microbial Communities Based on Terminal-Restriction Fragment Length Polymorphisms of 16S and 18S rRNA Genes. Microb Ecol 53, 562–570 (2007). https://doi.org/10.1007/s00248-006-9106-0

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  • DOI: https://doi.org/10.1007/s00248-006-9106-0

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