FlyBase Reference Manual Table of Contents

FlyBase .. Aberrations .. Anatomy .. BLAST .. Genes .. Annotation & Sequences .. Gene Products .. Maps .. People .. References .. Stocks .. Transposons
Help .. Searches .. News .. Site

RefMan Sections RefMan Table of Contents FlyBase Documents
FlyBase Reference Manual

Reference Manual A. Getting Started With FlyBase

A.1. What Is FlyBase?
A.2. How to Access FlyBase
A.3. How to Use FlyBase
A.4. How to Contact FlyBase
A.5. Learning More About FlyBase

Reference Manual B. Detailed Descriptions of FlyBase Structure and Data

B.1. Genes

B.1.1. General description of Genes data
B.1.2. List of Genes field descriptions
B.1.3. Detailed description of the Genes fields
B.1.4. Nontraditional alleles

B.1.4.1. Alleles of reporter genes
B.1.4.2. Alleles of ectopically expressed Drosophila gene products
B.1.4.3. Alleles of ectopically expressed non-Drosophila effector products
B.1.4.4. Classical alleles engineered into transposons, including rescue constructs

B.1.5. Protein and transcript symbols and exon naming
B.1.6. FlyBase Genes - Interactive Fly Cross Index
B.1.7. Differences and omissions from Lindsley and Zimm (1992)

B.2. Synonyms
B.3. Species other than D. melanogaster
B.4. Genetic objects from non-Drosophila species that are included in Drosophila
B.5. Maps

B.5.1. Gene Order Maps
B.5.2. Molecular Maps
B.5.3. Redbook Deficiency Maps

B.6. Computed Aberration Breakpoints and Cytological Locations of Genes

B.6.1. Notation
B.6.2. Proximity rather than Order
B.6.3. Provisos
B.6.4. Genome-derived Cytology

B.7. Wild genotypes and Chromosomes
B.8. Function and Structure of Gene Products
B.9. Aberrations

B.9.1. List of Aberrations field descriptions
B.9.2. Detailed description of the Aberrations fields

B.10. Transposons and transposon insertions
B.11. Stocks

B.11.1. Ordering stocks
B.11.2. Documentation for Individual Centers and Collections

B.11.2.1. The Bloomington Drosophila Stock Center at Indiana University
B.11.2.2. The European Drosophila Stock Center at Umeå (Umeå, Sweden)
B.11.2.3. The European Drosophila P-element-induced Lethal Stock Centre (Szeged, Hungary)
B.11.2.4. The Drosophila Species Stock Center
B.11.2.5. Stock lists from individual laboratories

B.12. Genomic Clones and STSs

B.12.1. Cosmids and cosmid STSs
B.12.2. P1 clones and P1 STSs
B.12.3. BAC clones and BAC STSs
B.12.4. Drosophila virilis P1 clones
B.12.5. YACs

B.13. References - the Drosophila Bibliography

B.13.1. Reference formats
B.13.2. Reference classes
B.13.3. Journals and multi-author works
B.13.4. Reference sources
B.13.5. Copyright statements

B.14. People
B.15. Anatomy and Images

Reference Manual C. Using FlyBase on the Web

C.1. Reaching the FlyBase Homepage
C.2. Report Options - Viewing FlyBase Data
C.3. FlyBase Search Tools

C.3.1. Simple Queries
C.3.2. All-options Queries

C.3.2.1. Examples of Genes Queries
C.3.2.2. Greek symbols in Queries
C.3.2.3. Other Database Accession Identifiers in Queries

C.3.3. Searching Stock Lists
C.3.4. Searching for Transposons and Transposon Insertions
C.3.5. Searching References
C.3.6. Multipurpose Search Tools

C.3.6.1. CytoSearch
C.3.6.2. Gene Expression Summaries
C.3.6.3. Anatomy Image Browser

Reference Manual D. Bulk FlyBase Data Retrieval

D.1. Bulk FlyBase data by Web query
D.2. Bulk FlyBase data by FTP

D.2.1. The file structure of FlyBase
D.2.2. Bulk data in ACODE and XML formats
D.2.3. Retrieving files

D.3. The FlyBase Gopher Server

Reference Manual E. Portable FlyBase Server
Reference Manual F. Links to and from FlyBase

F.1. FlyBase Identifier Numbers
F.2. Other links to FlyBase
F.3. Links to other molecular databases
F.4. Links to databases of other genomes

Reference Manual G. FlyBase Documentation

G.1. Genetic nomenclature of Drosophila
G.2. Controlled vocabularies used by FlyBase
G.3. FlyBase working papers
G.4. The Redbook

G.4.1. Lindsley and Zimm (1992) - The New Redbook
G.4.2. Redbook Errors
G.4.3. Lindsley and Grell (1968) - The Old Redbook

G.5. Greybook Errors - Ashburner (1989)
G.6. Personal communications to FlyBase
G.7. News

G.7.1. Announcements
G.7.2. Newsgroup bionet.drosophila
G.7.3. Drosophila Information Service (D. I. S.) subject indices
G.7.4. Drosophila Information Newsletter archive

Reference Manual H. Allied Data
Reference Manual I. The FlyBase Project

I.1. The copyright of FlyBase
I.2. How to reference FlyBase
I.3. How to contact FlyBase
I.4. The FlyBase Consortium
I.5. The FlyBase Advisors
I.6. Acknowledgments
I.7. Current problems

Send comments to us at flybase-help AT morgan.harvard.edu
FlyBase-NG uses Argos: A Replicable Genome infOrmation System