|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.