From: Charles Plessy Date: Fri, 18 Feb 2022 08:35:52 +0000 (+0900) Subject: LAST X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=f5b6ac496c267174f7f3d5f21feeca620242f17c;p=source.git LAST --- diff --git a/biblio/33346833.mdwn b/biblio/33346833.mdwn new file mode 100644 index 00000000..f27e4371 --- /dev/null +++ b/biblio/33346833.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Minimally-overlapping words for sequence similarity search."]] +[[!tag LAST method software alignment]] + +Frith MC, Noé L, Kucherov G. + +Bioinformatics. 2020 Dec 21;36(22-23):5344–50. doi:10.1093/bioinformatics/btaa1054. + +Minimally-overlapping words for sequence similarity search. + +[[!pmid 33346833 desc="Sparse seeds made of minimally overlapping words improve the speed with a good tradeoff on sensitivity. Describes the seeds RY4, …, RY32 used in LAST."]] diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn index 49e93fcd..f8ec88ea 100644 --- a/tags/LAST.mdwn +++ b/tags/LAST.mdwn @@ -2,8 +2,11 @@ _bibliography in progress..._ - - `lastdb` can use various seeding schemes to build its index. - [[Frith and Noé (2014)|biblio/24493737]] discuss some of them. + - `lastdb` can use various seeding schemes to build its index. [[Frith and + Noé (2014)|biblio/24493737]] discuss some of them. The `RY` seeds are made + of non-overlapping words using the two-letter alphabet `R` = `A|G`, `Y` = + `C|T`, to increase speed with a good tradeoff in sensitivity + ([[Frith MC, Noé L, Kucherov G, 2020|biblio/33346833]]). - `last-postmask` ([[Frith, 2011|biblio/22205972]]): discards alignments that contain a significant amount of lower-case-masked sequences.