Tools

From AAAWiki

Please post external tools or resources useful in the analysis of these 12 genome sequences here. In addition to a link, please include a brief description so people can quickly find what they are looking for.

Contents 1 Genome Databases 2 Gene Regulation 3 Transposable Elements 4 Miscellaneous

Genome Databases

• FlyBase THE Database of the Drosophila Genome
• DHGP The Drosophila Heterochromatin Genome Project
• DroSpeGe Drosophila Species Genomes
• BDGP Berkeley Drosophila Genome Project
• FlyMine FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans.

Gene Regulation

• ORegAnno Open Regulatory Annotation Database
• RedFly Regulatory Element Database for Drosophila from Gallo, Li, Hu and Halfon (2005) Bioinformatics 22:381-383.
• FlyReg This page provides access to results of the systematic curation and genome annotation of 1,365 DNase I footprints for the fruitfly D. melanogaster reported in Bergman, Carlson and Celniker (2005) Bioinformatics 21:1747-1749.
• FlyTF Drosophila transcription factor database.
• Bioinformatics Websites: Enhancers and binding sites
• Cross-species comparison of Affymetrix Dros2 Probesets

Transposable Elements

• REPET database providing Release 4 annotation of TEs in D. melanogaster
• BDGP Natural Transposable Element Project providing curated libraries of TEs in Drosophila
• REPBASE providing curated libraries of TEs.
• DHGP providing CAF1 TE prediction using PILER-DF and masked genomes and annotations using RepeatRunner

Miscellaneous

• CrossHair If you spend a lot of time staring at alignments on screen and you use Windows, then you almost certainly want this program.

• satellites/SSR predictions are available here