HOMD User Documentation     
Table of Content:
User Documentation
+Taxon Description
+Identify 16S rRNA Sequence
+Tools & Download
+Database Search
General Documentation
+HOMD Information
 > Important Notice Regarding Tannerella forsythia (strain 92A2)
 >Forsyth Scientists Support The Human Microbiome Project
 >HOMD 16S rRNA Reference Sequence Version 11.0 has been released
 >HOMD 16S rRNA Reference Sequence Version 13.0 has been released
 >HOMD Public Access Soon to be Announced
 >HOMD Public Release
 >HOMD publication available for download.
 >Press Coverage for HOMD
 >Publication: Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples
 >The Los Alamos ORALGEN Database Archive
Search Documentation:
Input Keywords:
Title Content
The Los Alamos ORALGEN Database Archive
Dear Oral/Dental Research Community:

It is my pleasure to announce to you that the Los Alamos ORALGEN Database has been restored and made available o­nline at http://www.oralgen.org

Many of you may have known that the ORALGEN database had been offline since some time last year. Thanks to Dr. Gang (Gary) Xie at the Los Alamos National Lab for providing the original content of the ORALGEN hard drive, I was able to restore the web service and make this important database available o­nline again to the research community.

Please note that this is an archival copy of the Los Alamos ORALGEN Database. This archival database is provided "as is", thus some links and tools may no longer work due to the changes of web address and server infrastructure. The primary purpose for making this archive available o­nline is for backtracking the citations/links that were published before. This database is no longer being maintained, nor is support provided. Many of the genomic sequences that were annotated by the ORALGEN has been updated and are different. Please visit http://www.homd.org/oralgen for a table listing and comparing these changes.

In addition to the availability of the original ORALGEN database, many researchers have also asked for the information with regards to the counterparts of the genes annotated by LANL ORALGEN, to those currently annotated by NCBI or HOMD. The information is important because many of the LANL ORALGEN annotated gene IDs had been cited in publications. For those genomes with sequences identical to those currently annotated by HOMD, we provide an "ORALGEN" panel in the newly implemented HOMD JBrowse genome viewer (http://www.homd.org/oralgen), so that users can match genes/proteins between HOMD/NCBI and ORALGEN directly in the genome viewer. For those genomes significantly different from the current HOMD/NCBI version, the coordination will be too different to be mapped in the genome viewer. This is especially true for these four genomes: Actinobacillus actinomycetemcomitans HK1651 (currently Aggregatibacter actinomycetemcomitans HK1651), Fusobacterium nucleatum polymorphum (Fusobacterium nucleatum subsp. polymorphum ATCC 10953), Streptococcus mutans UA159, and Tannerella forsythensis ATCC 43037.

For these genomes, the best way to find the equivalent genes annotated between HOMD/NCBI and ORALGEN is by protein homology. I am also providing the matching results in the The LANL ORALGEN FTP Archive (ftp://www.homd.org/lanl_oralgen). This FTP site contains the text data directly exported from the ORALGEN Database, including all the genomes and the associated information. The exported data are in Excel format and can be direct viewed as spreadsheets. Detail information for this archive is provided in the 00_README.txt file in the FTP site. In each of the folders of those 4 genomes with different sequences, there is an Excel file named "lanl_gene_id_2_ncbi_blastp.csv" or "lanl_gene_id_2_homd_blastp.csv". This table lists the possible counterparts of the ORALGEN genes to those in NCBI, (or HOMD) based o­n the BLASTP search. I hope this could ease some of the frustration that many of the researchers have been facing when they are trying to reconcile the differences between annotations.

Please do not hesitate to contact me if you have any question or concerns.


Tsute Chen, Ph.D.
Associate Research Investigator
Department of Molecular Genetics
The Forsyth Institute
245 First Street, Cambridge, MA

Article last modified on 2014-03-21 14:55:41 by tsute; viewed 194 times; Category: General Documentation; Topic: Announcement

Copyright 2007-2017 The Forsyth Institute