- Whole-genome alignments with reversed sequences as negative controls showed
that e-value filtering is not enough to remove spurious alignments of tandem
repeat which therefore need to be masked ([[Frith MC, Hamada M and Horton P.,
- 2011|bilbio/20144198]]).
+ 2011|biblio/20144198]]).
- `lastdb` can use various seeding schemes to build its index. [[Frith and
NoƩ (2014)|biblio/24493737]] discuss some of them. The `RY` seeds are made
of expansion of tandem repeats, after alignment with `last-split`.
- LAST can align DNA sequences to protein databases using a 64 x 21 substitution
- matrix [[Yao and Frith, 2020|biblio/10.1101_2021.01.25.428050]].
+ matrix [[Yao and Frith, 2020|biblio/10.1007_978-3-030-74432-8_11]].
- JRA (Joint Read Alignment) uses LAST [[Shrestha and coll., 2018|biblio/29182778]].