Algal Pathway/Genome Databases |
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This website contains 13 Algal genomes and associated metabolic pathways. This website is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes. Click on the "Change Current Database" button (above) to explore the available databases.
This site includes extensive retrieval, visualization and analysis tools, including a Genome browser and a metabolic map diagram. There are tools for analysis of gene expression, metabolomics and ChIP-chip data. You can search and align sequences for Chlamydomonas reinhardtii and other genomes and perform comparative analysis. You can store groups of genes and pathways into a SmartTable, and then browse, analyze and share with other users.
What people are saying
"BsubCyc is a tool of the utmost value."

Paul Babitzke
Prof. of Biochemistry
& Molecular Biology
"My lab uses these resources on a daily basis."

Patricia Kiley,
Professor and Chair,
Dep't. of Biomolecular Chemistry
"We rely on BioCyc's Gene Pages and Overview Diagrams almost daily."

Arkady Khodursky
Assoc. Prof. Biochemistry
"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."

William Cannon, Team Lead
Computational Biology
"BioCyc is the go-to resource of knowledge and tools for Ginkgo scientists."

"BioCyc is a tremendous resource for pathway analysis in metabolomics."

Art Edison, Dept of Genetics
"We make extensive use of the BioCyc full metabolic network diagram for omics data analysis."

Timothy J. Donohue, Director
"I have not found another database that has a better interface than BioCyc."

Gary B. Huffnagle, Professor
Microbiology and Immunology
Learning Library
Webinar Series
Webinar #1: Introduction to BioCyc
- BioCyc Overview Part 1 (14:04) [mp4 video] or [YouTube]
- Searching in BioCyc (17:00) [mp4 video] or [YouTube]
- Genome Browsing, Searching, and Alignment (15:38) [mp4 video] or [YouTube]
- Pathways (13:19) [mp4 video] or [YouTube]
- Reactions (3:37) [mp4 video] or [YouTube]
- Compounds (6:42) [mp4 video] or [YouTube]
Webinar #2: Introduction to SmartTables
- Part 1: SmartTables Overview (4:30) [mp4 video] or [YouTube]
- Part 2: SmartTables Basics (12:43) [QuickTime Video]
- Part 3: SmartTables Transformations (8:08) [QuickTime Video]
- Part 4: SmartTables Import and Export (9:00) [QuickTime Video]
- Part 5: SmartTables Gene Expression Analysis (7:40) [QuickTime Video]
- Part 6: Metabolomics Analysis with SmartTables (6:45) [QuickTime Video]
Webinar #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
- Part 1: The Cellular Overview: Navigating metabolic networks (17:15) [mp4 video] or [QuickTime Video] or [YouTube]
- Part 2: Comparative Genomics (21:06) [Windows Media Video] or [QuickTime Video]
- Part 3: Ortholog Viewing (10:02) [Windows Media Video] or [QuickTime Video]
- Part 4: The Regulatory Overview -- exploring transcriptional regulatory networks (15:21) [mp4 video] or [YouTube]
Webinar #4: Omics Data Analysis
- Transcriptomics Analysis Tools [brief tour (2:40) mp4 video or YouTube] [detailed tutorial (21:36) mp4 video or YouTube]
- Metabolomics Analysis Tools [brief tour (3:26) mp4 video or YouTube] [detailed tutorial (24:09) mp4 video or YouTube]
- Omics Dashboard Part 1 (16:35) [mp4 video], or [YouTube]
- Omics Dashboard Part 2 (24:29) [mp4 video], or [YouTube]
Webinar #5: Pathway Collages
- Pathway Collages (22:39) [mp4 video], [QuickTime Video] or [YouTube]
Webinar #6: Creating a Pathway/Genome Database
- Part 1A: Introduction to Database Building and Pathologic (14:04) [MP4 Video] or [YouTube]
- Part 1B: Building a Database: Detailed Pathologic Example (23:53) [MP4 Video] or [YouTube]
- Part 2A: General Editing Strategies (8:00) [Windows Media Video] or [QuickTime Video] or [YouTube]
- Part 2B: Creating and Editing Reactions and Compounds (17:32) [Windows Media Video] or [QuickTime Video] or [YouTube]
- Part 2C: Updating Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10) [Windows Media Video] or [QuickTime Video] or [YouTube]
- Part 2D: Making and Editing Pathways (9:42) [Windows Media Video] or [QuickTime Video] or [YouTube]
Webinar #7: Using the Structured Advanced Query Page
- Quick Introduction (6:27): "Structured Advanced Query Page Quick Introduction" [Windows Media Video] or [mp4 video] or [YouTube]
- Full Webinar (42:15): "Structured Advanced Query Page" [Windows Media Video] or [mp4 video] or [YouTube]