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| | The Human Oral Microbial Genomes in HOMD | This page is the overview and describes the categories of the genomes listed in HOMD. For the features and explanation of the tables that list the genomes in different categories, please refer to the article "Genome Tables".
HOMD aims to provide the most comprehensive information for all the human oral microbes as well as the genomics tools that are available. All the human oral microbial taxa in HOMD were defined and classified based on the 16S rRNA sequences. Some taxa defined may only have the 16S rRNA sequences available (which were sequenced from PCR products amplified from clinical samples) let alone extracting genomic DNA from cultures for sequencing. Thus not all human oral taxa have strains that have been or are being sequenced. The human oral microbial genomes that are listed in HOMD have different amounts of information and various types of software tools available. The HOMD genomes are organized in the following major categories:
1) Genomes Annotated at HOMD: Genome Surveys
One major goal of HOMD is to partially sequence up to 100 representative human oral microbial species. These genomes with sequences directly generated by the HOMD project is termed the HOMD Survey Genomes. These partial genomic sequences are fully annotated by the HOMD automatic annotation pipeline; and are listed under the category called "Genomes Annotated at HOMD : Genome Surveys".
2) Genomes Annotated at HOMD: Full Genomes
The second category "Genomes Annotated at HOMD : Full Genomes" are for those oral microbial species that have been fully sequenced by other institutes. Genomes of several of the important oral microbial pathogens have been fully decoded and static annotations have been available (e.g., at NCBI). For these publicly available genomic sequences, we periodically re-annotated the entire genome and provide users with the most up-to-date annotation as well as the convenience of viewing different annotations (e.g., NCBI annotation or JCVI annotation, if available) in the HOMD Genome Viewer.
3) Genomes Annotated at HOMD: Metagenomes
The third category "Genomes Annotated at HOMD : Metagenomes" are partial sequences of human oral microbes that have been generated by other institutes. This category will grow significantly in the near future once the sequences generated by the "Human Microbiome Project" start to kick in. HOMD intends to periodically annotate these metagenomic sequences when they are made publicly available. The re-annotation frequencies will be determined by the total amount of the sequences and the capacity of HOMD computer servers.
4) Genomes Annotated Elsewhere: Full Genomes
The fourth category "Genomes Annotated Elsewhere: Full Genomes" list all other human oral microbial genomes that are not currently in the HOMD annotation pipeline. Although HOMD aims to annotate all human oral microbial genomes, some microbial species identified in human oral cavities can only be considered transient species and thus are not included in the annotation pipeline. To name only two of many examples, there are many strains of Escherichia coli and many species of Pseudomonas, for which their full genome are sequenced and static annotation available at NCBI. Although these species are also found in human oral cavities, their primary niches in human body is by no mean oral, nor do they have any known association with oral infectious diseases. These transient oral species, though are described in the HOMD Taxonomy database, are not annotated by the HOMD pipeline. We do however provide the viewing and searching capabilities for the static annotation information in the Genome Viewer for these genomes.
In addition, so far sequences listed in this category are all full genomes - genomes for which the sequences have been completed decoded. Partial genomic sequence of the transient oral taxa may also be available but are rarely annotated. At the present time, HOMD is the only database that provides annotations for partial genomic sequences.
5) Genomes in Progress
Any other human oral taxa, indigenous or transient, if the genomic sequences are still being determined or there is any information regarding the plan for sequencing, will be listed in this category. The information listed in this category is gathered first automatically by a computer program every other week from major genomic sequence databases such as Genome online and NCBI Genome Survey and Genome Projects databases. The automatically generated information is then curated manually before enlisted in this table.
6) All HOMD Genomes
This category non-redundantly combines all categories mentioned above and provides an alternative interface for users seeking a particular genome.
For the features and explanation of the tables that list the genomes in different categories, please refer to the article "Genome Tables". | | Article last modified on 2008-02-22 14:58:20 by wenhan; viewed 868 times; Category: User Documentation; Topic: Genomes |
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