silva ribosomal rna database
DESCRIPTION
A short presentation about Silva rRNA database. Silva provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).TRANSCRIPT
BioInformatics, 27 November 2014, Cluj-Napoca, Romania
quality checked and aligned ribosomal RNA sequence data
http://www.arb-silva.de/
Călin G. FLOARE
BioInformatics, 27 November 2014, Cluj-Napoca, Romania
Outline
Why rRNA sequence data
16S rRNA
Silva database
mothur use Silva
Human Microbiome Project (HMP)
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Why rRNA sequence data
Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction,
nucleic acid based detection and
quantification of microbial diversity.
Ribosomal Database Project (RDP-II)
http://http://rdp.cme.msu.edurdp.cme.msu.eduhttp://www.arbhttp://www.arb--silva.desilva.de//
SILVA quality checked and aligned ribosomal RNA sequence data
rRNA specific databasesrRNA specific databases
SILVA quality checked and aligned ribosomal RNA sequence data
rRNA specific databases
http://www.arbhttp://www.arb--silva.desilva.de//
SILVA quality checked and aligned ribosomal RNA sequence data
rRNA specific databases
http://www.arbhttp://www.arb--silva.desilva.de//
SILVA quality checked and aligned ribosomal RNA sequence data
rRNA specific databases
Ribosomal Database Project (RDP-II)
http://www.arbhttp://www.arb--silva.desilva.de//
SILVA quality checked and aligned ribosomal RNA sequence data
rRNA specific databases
2/19
BioInformatics, 27 November 2014, Cluj-Napoca, Romania
16S ribosomal RNA (or 16S rRNA) is a component of the 30S small subunit of prokaryotic 70S ribosomes.
16S rRNA gene sequencing is considered by current taxonomists to be the gold standard in bacterial identification and classification.
16S rRNA gene contains conserved regions useful for the design of universal PCR primers that can amplify various fragments of the 16S rRNA gene from all pathogenic and nonpathogenic bacteria. These fragments include hypervariable regions containing species-specific signature sequences useful for bacterial identification to species level.
In some instances, alternate genes such as hsp65, rpoB or recA are sequenced when 16S is not adequate for species level identification.
http://http://depts.washington.edu/molmicdx/mdx/tests/bctseq.shtmldepts.washington.edu/molmicdx/mdx/tests/bctseq.shtml
16S rRNA
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16S rRNA
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http://http://rna.ucsc.edu/rnacenter/ribosome_images.htmlrna.ucsc.edu/rnacenter/ribosome_images.html
BioInformatics, 27 November 2014, Cluj-Napoca, Romania
Silva
Silva (from Latin silva, forest), was implemented to provide a central comprehensive up to date web resource of aligned small (16S/18S,SSU) and large (23S/28S, LSU) subunit ribosomal RNA (rRNA) sequences from the Bacteria, Archaea and Eukarya domains.
Release 119 contain full length sequences and taxonomy references for 137879 bacteria, 3155 arches, and 12273 eukarya (~7.2Gb).
All sequences are
checked for anomalies,
carry a rich set of sequence associated contextual information,
have multiple taxonomic classifications, and
contain the latest validly described nomenclature.
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Mothur use Silva
mothur is currently the most cited bioinformatics tool for analyzing 16S rRNA gene sequences
can be used to process data generated by Sanger, PacBio, IonTorrent, 454, and Illumina(MiSeq/HiSeq)
http://http://www.mothur.orgwww.mothur.org
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Mothur is an open-source, platform-independent, community-supported software for describing and comparing microbial communities.
An analysis of 8 marine samples of more than 222,000 16S rRNA gene sequences was completed in less than 2 hours with a laptop computer.
doi: 10.1128/AEM.01541-09
BioInformatics, 27 November 2014, Cluj-Napoca, Romania
Human Microbiome Project (HMP)
Our SelfOur Self--Portrait: the Human Portrait: the Human MicrobiomeMicrobiome
www.nature.com/nature/journal/v486/n7402/www.nature.com/nature/journal/v486/n7402/https://www.broadinstitute.org/news/4199https://www.broadinstitute.org/news/4199
The microbiome are the bacteria living on and within us. Like the rainforest, the healthy human microbiome is a balanced ecosystem. The correct balance of microbes keep potential pathogens in check and regulate the immune system. Microbes also perform essential functions such as digesting food and synthesizing vitamins.
The goal of the Human Microbiome Project is to characterize the human microbiome and analyze its role in human health and disease.
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http://www.hsph.harvard.edu/news/press-releases/human-microbiome-project/files/hmptree_121.pdf
“each person’s microbial signature is fairly unique, in much the same way that an individual’s genome is unique,” Curtis Huttenhower
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Thank you for your attention