Fruitfly Bioinformatics Resources

Fruitfly bioinformatics resources

Bioinformatics resources for multi-species fruitfly comparative genomics.

Mailing lists and wiki

• Multiple@fruitfly.org mailing list

• "AAA" fruitfly annotation wiki
  • http://rana.lbl.gov/drosophila/wiki/index.php/Main_Page

• Holmes lab fruitfly wiki (all of the action's at the AAA wiki, you probably want to go there instead)
  • http://fly.biowiki.org/

Fruitfly genome alignments: 12 Drosophila species

These links are now a little out of date. See AAA:Alignment for a current list. Ian Holmes - 15 Apr 2006

• MAVID (Pachter, Dewey; UC Berkeley)
• MAUVE (Perna, Darling; UW-Madison)
• MLAGAN (Iyer, Pollard, Eisen; UC Berkeley/LBNL)
• MULTIZ (UCSC)
• VISTA (Dubchak et al, LBNL)

Annotations

These links are available at AAA:Annotation which is more regularly updated. Ian Holmes - 15 Apr 2006

• Flybase annotations
  • http://flybase.bio.indiana.edu/annot/

• GBrowse images
  • http://insects.eugenes.org/species/cgi-bin/gbrowse_img/
  • http://rana.lbl.gov/cgi-bin/gbrowse_img/
  • http://wwwfgu.anat.ox.ac.uk:8080/cgi-bin/gbrowse_img/

• Probabilistic gene predictions
  • N-scan: http://genes.cs.wustl.edu/private/Drosophila

People

• Mike Eisen group
  • AAA page: Assembly, Alignment and Annotation of 12 fruitfly genomes
    • Assemblies
    • Alignments
    • Annotations
  • Evolutionary trees
  • GBrowse images

• Lior Pachter group
  • MERCATOR/MAVID alignments
    • alignment and homology mapfile formats documented here
  • Genemapper annotations: http://bio.math.berkeley.edu/genemapper/fruitfly.html

• Chris Ponting group
  • Gene predictions from Andreas Heger

• Don Gilbert group
  • Insert for JBrowse.conf that will add view frames from DroSpeGe

• Ian Holmes' group
  • Phylogenies, reversible and irreversible rate matrices for nine-species MAVID alignments. Branch lengths and rate matrices were estimated using the xrate program on a per-alignment basis, starting from the tree topologies produced by Dan Pollard. (The rate matrices are the "general reversible" and "general irreversible" models.)
  • Pfold scan for conserved RNA structure
  • More references for fruitfly transposons