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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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dc.contributor.authorShyu, C.
dc.contributor.authorSoule, T.
dc.contributor.authorBent, S.
dc.contributor.authorFoster, J.
dc.contributor.authorForney, L.
dc.date.issued2007
dc.description.abstractA 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/.
dc.description.statementofresponsibilityConrad Shyu, Terry Soule, Stephen J. Bent, James A. Foster and Larry J. Forney
dc.identifier.citationMicrobial Ecology: an international journal, 2007; 53(4):562-570
dc.identifier.doi10.1007/s00248-006-9106-0
dc.identifier.issn0095-3628
dc.identifier.issn1432-184X
dc.identifier.orcidBent, S. [0000-0003-1563-2855]
dc.identifier.urihttp://hdl.handle.net/2440/66455
dc.language.isoen
dc.publisherSpringer-Verlag
dc.rights© Springer Science + Business Media, LLC 2007
dc.source.urihttps://doi.org/10.1007/s00248-006-9106-0
dc.subjectRNA, Ribosomal, 16S
dc.subjectRNA, Ribosomal, 18S
dc.subjectRestriction Mapping
dc.subjectPolymerase Chain Reaction
dc.subjectSequence Analysis, DNA
dc.subjectComputational Biology
dc.subjectMicrobiology
dc.subjectPolymorphism, Restriction Fragment Length
dc.subjectInternet
dc.subjectSoftware
dc.subjectDatabases, Nucleic Acid
dc.titleMiCA: A web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes
dc.typeJournal article
pubs.publication-statusPublished

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