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The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.

The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD--taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org.

Pubmed ID: 20624719 RIS Download

Mesh terms: Bacteria | Computers | Databases, Genetic | Genome, Bacterial | Humans | Internet | Metagenome | Metagenomics | Mouth | Phenotype | RNA, Bacterial | RNA, Ribosomal, 16S | Sequence Alignment | Software

Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.

This is a list of tools and resources that we have found mentioned in this publication.


Genomes Online Database

Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data.

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European Bioinformatics Institute

A non-profit academic organization for research and services in bioinformatics that provides freely available data from life science experiments, performs basic research in computational biology, and offers an extensive user training programme, supporting researchers in academia and industry. The Institute manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures.

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HMP Data Analysis and Coordination Center

The Data Analysis and Coordination Center (DACC) for the Human Microbiome Project (HMP) is the central repository for all HMP data. The aim of the HMP is to characterize microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health. The HMP DACC Data Browse interface provides a means to search and download data sets generated by the HMP. The data is presented in a simple directory hierarchy. This directory includes production and validation sub-projects, each linked to their respective data sets. The current functionality allows you to link to the NCBI HMP datasets or to download bulk datasets provided by the DACC. Software and online resources used in, or developed as part of the HMP as well as protocols describing new advances & technologies are posted as they become available. Protocols or software packages that you would like to post on this site are welcome.

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NCBI

A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.

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BioEdit

A biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7.

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HPV Sequence Database

THIS RESOURCE IS NO LONGER SUPPORTED, documented August 23, 2016. The Human Papillomaviruses Database collects, curates, analyzes, and publishes genetic sequences of papillomaviruses and related cellular proteins. It includes molecular biologists, sequence analysts, computer technicians, post-docs and graduate research assistants. This Web site has two main branches. The first contains our four annual data books of papillomavirus information, called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. and the second contains papillomavirus genetic sequence data. There is also a New Items location where we store the latest changes to the database or any other current news of interest. Besides the compendium, we also provide genetic sequence information for papilloma viruses and related cellular proteins. Each year they publish a compendium of papillomavirus information called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. which can now be downloaded from this Web site.

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Washington University Basic Local Alignment Search Tool

It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterized genes.

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BLAST Assembled RefSeq Genomes

This portal takes you to the NCBI''s BLAST Assembled RefSeq Genomes. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Sponsors: This resource is supported by the National Institutes of Health. Keywords: BLAST, Genome, Search engine, Sequence, Biological, Local, Alignment, Nucleotide, Protein, Program, Database, Stastical, Functional, Evolutionaary, Gene,

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ExPASy

A bioinformatics resource portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, structural bioinformatics, systems biology, phylogeny, evolution, population genetics, transcriptomics, biophysics, imaging, IT infrastructure, and drug design. On this portal users can find resources from many different SIB groups as well as external institutions.

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