Topic: Public Documents

The new items published under this topic are as follows.

Documentation: Scripts for Generating Circular Transcriptome Maps from RNAseq Data

Posted by: tsute on Wednesday, March 14, 2012 - 04:59 PM
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Read full article: 'Scripts for Generating Circular Transcriptome Maps from RNAseq Data' (3028 bytes more)

Announcement: New BROP Interface and Tools Coming Soon!

Posted by: tsute on Friday, June 01, 2007 - 03:05 PM
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We are actively working on a new home page design and interface for BROP. The new design will have easier accesses to all the tools and databases available at BROP. During the transition stage, you may encounter some problems with some links. We apologize for the inconvenience this may cause. We look forward to complete this redesign pretty soon. Please check here often for any update. You are also welcome to subscribe to the BROP MAILING LIST to receive updates in your email.

Introduction to BROP

Posted by: tsute on Friday, June 01, 2007 - 02:42 PM
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Welcome to The Bioinformatics Resource for Oral Pathogen (BROP). BROP aims to provide to the international scientific research community an online bioinformatics resource center that is specialized in oral pathogens and oral infectious diseases. BROP is integrative, current, and community-centric. By integrative, we mean that all the tools and information provided by BROP are seamlessly linked together. For example, the SAOPMD microarray analysis result provides links for individual genes back to the BROP Genome Viewer. By current, we update the genomic annotations at a very frequent rate with the BROP Automatic Genomic Annotation Pipeline. By community-centric, BROP also serves as a platform for scientific discussion, collaboration, data storage, sharing, and management. The myOPMD project is an initial example of such a platform. By becoming an integrative, current and community-centric resource center, BROP will help to accelerate our understanding toward the oral pathogens and the associated diseases.

Announcement: MyOPMD and SAOPMD - microarray data analysis and management tools

Posted by: admin on Thursday, March 02, 2006 - 03:20 PM
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MyOPMD and SAOPMD are two new microarray data analysis and management tools specially designed for oral pathogen microarrays and are available now for use ...

Read full article: 'MyOPMD and SAOPMD - microarray data analysis and management tools' (1902 bytes more)

Announcement: EMBOSS Software Package Available at BROP

Posted by: admin on Wednesday, January 18, 2006 - 06:06 PM
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BROP is now providing the complete EMBOSS Software Package for analyzing the oral pathogen sequences. EMBOSS stands for "The European Molecular Biology Open Software Suite". It is a free Open Source software analysis package and contains more than 150 applications for analyzing the molecular sequences. [Quick visual demo].

Announcement: Genome Explorer New Tool

Posted by: admin on Thursday, November 10, 2005 - 02:42 AM
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Now you can retrieve a specified range of any BROP geonomes (both oral pathogens and NCBI microbial genomes) while you view them in the Genome Viewer. Click here for an illustrated example.

Announcement: Two BROP Abstracts presented in 2005 IADR Annual Meeting

Posted by: admin on Wednesday, March 02, 2005 - 09:58 PM
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Read full article: 'Two BROP Abstracts presented in 2005 IADR Annual Meeting' (4286 bytes more)

Documentation: OPMD Home

Posted by: admin on Saturday, February 19, 2005 - 02:22 AM
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Oral Pathogen Micorarray Database (OPMD) Public Access or Log in with an account

Data Analysis Tools for Oral Pathogen Microarray data

Documentation

Documentation: OPMD Home

Posted by: admin on Saturday, February 19, 2005 - 02:21 AM
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Data:
- MyOPMD: An Online Microarray Data Management Tools
- Oral Pathogen Micorarray Database (OPMD) Public Access or Log in with an account
- Supplemental Data in Publications
Tools:
- Significance Analysis of Oral Pathogen Microarray Data (SAOPMD)
- View Porphyromonas gingivalis microarray data in BROP Genome Viewer
Documentation:
- OPMD User's Guide
- SAOPMD User's Guide
- MyOPMD User's Guide
- Array Information

Documentation: Genome Home

Posted by: admin on Saturday, February 19, 2005 - 02:21 AM
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BROP Genomics Tools and Databases (User's Guide)

Available Tools and Databases at BROP

<tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Actinobacillus
actinomycetemcomitans <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Actinomyces naeslundii <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Fusobacterium nucleatum ATCC 10953 <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Fusobacterium nucleatum ATCC 25586 <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Porphyromonas gingivalis <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Prevotella intermedia <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Streptococcus gordonii <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Streptococcus mitis <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Streptococcus mutans <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Streptococcus sanguis <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Streptococcus sobrinus <td colspan="7">

Not yet available

<tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Tannerella forsythensis <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Treponema denticola <tr bgcolor="#FFFFFF"> <td bgcolor="#FFFFFF">Treponema lecithinolyticum†‡

<font color="#FFFFFF">Organism Name
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />
<input type="button" value="Genome Viewer" class="formbutton0" />	<input type="button" value="View Dynamic Annotation" class="formbutton0" />	<input type="button" value="Blast Against Genome" class="formbutton0" />	<input type="button" value="wEMBOSS" class="formbutton0" />	<input type="button" value="KEGG" class="formbutton0" />	<input type="button" value="GO" class="formbutton0" />

<font color="#00CC00">†	Unfinished genome contigs that include assembled sequence contigs as well as unassembled single sequence reads (singlets)
<font color="#FF00FF">‡	The annotation includes partial ORF sequences that have no start or stop codon identified at both ends of contigs or singlets
<font color="#CC3300">§	OPMD: Oral Pathogen Microarray Database