Whole genome alignment

Two types of pairwise genome alignment are available in Ensembl Genomes, based on LastZ [1] (or its predecessor BlastZ [2]) and translated BLAT (tBLAT) [3]. LastZ is typically used for closely related species, and tBLAT for more distant species. The method of alignment affects the coverage of the genomes, with tBLAT expected to mostly find homologies in coding regions.

The raw results from LastZ or tBLAT are alignment blocks, which are 'chained' according to their location in both genomes, then 'netted' to choose the best sub-chain in each region for the reference species [4]. The resultant LastZ-net and tBLAT-net alignments are displayed in Ensembl Genomes for selected fungal, metazoan, protist and plant species.


  1. Improved pairwise alignment of genomic DNA. Harris RS. 2007. Ph.D. Thesis, The Pennsylvania State University.
  2. Human-mouse alignments with BLASTZ. Schwartz S et al. 2003. Genome Research. 13(1):103-7.
  3. BLAT--the BLAST-like alignment tool. Kent WJ. 2002. Genome Research. 12(4):656-64.
  4. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Kent WJ et al. 2003. PNAS. 100(20):11484-9.