Daniel Pollard and Venky Iyer
Eisen Lab at UC Berkeley and LBNL
July 20 2005

Intergenic Alignments for D.melanogaster against D.simulans, D.erecta, D.yakuba, D.ananassae, D.pseudoobscura, D.virilis and D.mojavensis.

These alignments are made using a combination of synteny based and BLAST-based methods to find the orthologous region; MLAGAN (Brudno/Batzoglou) was used to align the orthologous sequences. The tarballs contain one multi-FASTA alignment file per D.mel region, named with its Flybase release 4.0 coordinates. Species are missing from this file if no orthologous sequence that passed a quality threshold was found. The heuristic quality threshold was set by examining the quality of alignments of random sequences. Please contact Daniel Pollard or Venky Iyer if you have questions.

Chromosome 2L
Chromosome 2R
Chromosome 3L
Chromosome 3R
Chromosome 4
Chromosome X