Main Page
From MaizeSequence
Welcome to the Maize Sequence wiki
This wiki is meant to be an internal knowledge base for the CSHL team of Maize Genome Sequencing Project
Contents |
Browser
- Visualizing contig order and orientation in Ensembl
- Browser Implementation Plan
- Questions for the Public
- Browser Software Release Plan
- Browser Reviewers
- List of Tracks
- Entry Page Requirements
- Loading FPC Map into CytoView
- Hardware Environments
- Working Document
- Browser Navigation Bar
- Maize Notification System
- Browser Use-Cases
- FAQ Items for Sandy Clifton and Anne Sylvester
Papers
BAC Analysis
- Annotation Pipeline Checklist
- Levels of BAC Annotations
- Annotation Flowchart
- Data Quality Control
- FGENESH Gene Prediction Nomenclature
- Peptide Classification Protocol
- Setting up the Ensembl annotation pipeline
- Workflow from Clonepath to an Annotated Ensembl Database
- FgeneshGene.pm Module
- Running Protein Annotations
- Exonerate
- BLAT Sequence Alignment Parameters
- Non-coding RNA Analyses
- Working_Gene_Set
- Attributes fields
Quality Control
Important Links
- Maize Browser
- Maize Browser (Development)
- Internal Gbrowse: Maize FPC
- Internal Gbrowse: Maize BACs
- Mantis: Bug and Feature Tracker
Documents
- Maize Assembly
- Working Gene Set
- Maize Versioning Scheme
- Maize Project Challenges
- Maize Progress Reports
- Maize Subprojects
- Project Milestones
- Clonepath Database Schema
- BAC Statuses
- Maize Marker Categories
- Browser Requirements
- Maize Project abstracts
- Related Literature
- NSF Maize Call for Papers
- Repeat Analysis with Phillip San Miguel
- Maize Project Repeat Annotation
- Gene Class Discrimination
- Josh's GeneBuild Comments
- Maize Genome Sequencing Consortium
- Linda's Maize Sequence Statistics for Maize SAB 2007
- Josh's evaluation of exonerate based on browser
- Biopipe Cereal Alignment Issues and troubleshootings
- How To Deal With Cotton BACs
- Accelerated Region
- Whole Genome Alignments
- Browser Brochure
Presentations
- Shiran: Maize Project Status
- October 4, 2007: Stein/Ware lab group meeting presentation
- Shiran: Hershey Bioinformatics Seminar
- January 17, 2007
- Josh: Delbruck Seminar
- January 23, 2007
Meetings
- Wednesday, November 26, 2008
- Wednesday, October 29, 2008
- Wednesday, October 8, 2008
- Wednesday, August 20, 2008
- Wednesday, August 6, 2008
Collaborations
Administration
Software Development
- Upgrading EnsEMBL
- Ensembl 38 Migration
- Version Configuration Management
- Maize MySQL Databases
- HOWTO:Add Legend to Ensembl
