MiCA: A Web-Based Tool for the Analysis of Microbial Communities Based on Terminal-Restriction Fragment Length Polymorphisms of 16S and 18S rRNA Genes
| Autor: | Larry J. Forney, Conrad Shyu, Terry Soule, Stephen J. Bent, James A. Foster |
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| Rok vydání: | 2007 |
| Předmět: |
Genetics
Internet Ecology Sequence analysis Restriction Mapping Computational Biology Soil Science Sequence Analysis DNA Ribosomal RNA Biology Microbiology Polymerase Chain Reaction Restriction site Restriction enzyme Terminal restriction fragment length polymorphism Restriction map RNA Ribosomal 16S RNA Ribosomal 18S Restriction fragment length polymorphism Databases Nucleic Acid Polymorphism Restriction Fragment Length Software Ecology Evolution Behavior and Systematics In silico PCR |
| Zdroj: | Microbial Ecology. 53:562-570 |
| ISSN: | 1432-184X 0095-3628 |
| DOI: | 10.1007/s00248-006-9106-0 |
| Popis: | 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/. |
| Databáze: | OpenAIRE |
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