Whole genome alignment Tutorial

Two types of pairwise genome alignment are available in VectorBase, based on LastZ [1] and translated BLAT (tBLAT) [2]. 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 [3].

Coverage statistics are available for all pairwise alignments (e.g. Anopheles gambiae and Anopheles coluzzii).

References

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

Data Access

Pairwise alignments are viewable in the genome browser, and are also available for download in bulk.