From 117ff9b209855fae677e69d5079bfdcd4aaddbf7 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Wed, 25 Jan 2023 15:50:57 +0900 Subject: [PATCH] progressive cactus --- biblio/33177663.mdwn | 10 ++++++++++ tags/alignment.mdwn | 6 +++++- 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 biblio/33177663.mdwn diff --git a/biblio/33177663.mdwn b/biblio/33177663.mdwn new file mode 100644 index 00000000..a709cf61 --- /dev/null +++ b/biblio/33177663.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Progressive Cactus is a multiple-genome aligner for the thousand-genome era."]] +[[!tag genome alignment]] + +Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, Lindblad-Toh K, Haussler D, Karlsson E, Jarvis ED, Zhang G, Paten B. + +Nature. 2020 Nov;587(7833):246-251. doi: 10.1038/s41586-020-2871-y + +Progressive Cactus is a multiple-genome aligner for the thousand-genome era + +[[!pmid 33177663 desc="Aligns with cactus 2~5 genomes, in- and out-group, and reconstitutes an ancestral genome. Recurses the phylogenetic tree progressively. A ‘best-hit-filtering’ step is added to catch duplications that are not seen in the outgroups. Also runs a step ‘removing recoverable chains’ to allow for corrections and mitigate error propagation. Aligning 600 amniotes took ~2 months."]] diff --git a/tags/alignment.mdwn b/tags/alignment.mdwn index 2bbe4c8b..6e7a6619 100644 --- a/tags/alignment.mdwn +++ b/tags/alignment.mdwn @@ -8,8 +8,12 @@ see [[LAST]] for a detailed bibliography. ## Cactus - - Paten and coll, ([[March 2011|biblio/21385048]]) describe _cactus_ graphs + - Paten and coll., ([[March 2011|biblio/21385048]]) describe _cactus_ graphs where nodes are sets of adjascencies and edges are aligned blocks of sequences. A genome can be represented as path in these graphs. + - Armstrong and coll. ([[2020|biblio/33177663]]) describe _progressive cactus_, + an iterative approach where ancestral genomes are reconstituted using 2-5 pairs + of in- and out-group comparisons, and then progressively aligned to each other. + [[!inline pages="tagged(alignment)" limit=0]] -- 2.47.3