From: Charles Plessy Date: Fri, 15 Apr 2022 06:25:22 +0000 (+0900) Subject: Café X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=1d23e5fd3a837eec82b7537865a17ae38e7ac441;p=source%2F.git Café --- diff --git a/biblio/20144198.mdwn b/biblio/20144198.mdwn new file mode 100644 index 00000000..30d63bb9 --- /dev/null +++ b/biblio/20144198.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Parameters for accurate genome alignment."]] +[[!tag LAST genome alignment]] + +Frith MC, Hamada M, Horton P. + +BMC Bioinformatics. 2010 Feb 9;11:80. doi: 10.1186/1471-2105-11-80 + +Parameters for accurate genome alignment. + +[[!pmid 20144198 desc="Aligned genomes after reversing (not reverse-complementing) them as a negative controls. In these comparisons, all alignments are spurious. A large number of spurious alignments were found, and this could be reduced by masking tandem repeats. Spuriously alignments in tandem repeats get abnormally high scores. “Bad” scoring matrices tend to extend alignments with spurious low-quality arms. The X-drop parameter prevents the aligner from extending alignments too far, but high X-drop values can cause small alignments to be discarded by some software because the score becomes negative."]] diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn index f8ec88ea..8157f372 100644 --- a/tags/LAST.mdwn +++ b/tags/LAST.mdwn @@ -2,6 +2,11 @@ _bibliography in progress..._ + - 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]]). + - `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` =