From 4714fb72375e4410abdce9561bb97c5d745b00cd Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Tue, 24 Jan 2023 09:35:43 +0900 Subject: [PATCH] Cactus --- biblio/21385048.mdwn | 13 +++++++++++++ tags/alignment.mdwn | 15 +++++++++++++-- 2 files changed, 26 insertions(+), 2 deletions(-) create mode 100644 biblio/21385048.mdwn diff --git a/biblio/21385048.mdwn b/biblio/21385048.mdwn new file mode 100644 index 00000000..77e98664 --- /dev/null +++ b/biblio/21385048.mdwn @@ -0,0 +1,13 @@ +[[!meta title="Cactus graphs for genome comparisons."]] +[[!tag genome alignment]] + +Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D. + +J Comput Biol. 2011 Mar;18(3):469-81. doi: 10.1089/cmb.2010.0252 + +Cactus graphs for genome comparisons. + +[[!pmid 21385048 desc="Alignments are transformed in sequence graphs where +nodes are connected by either alignment blocks or adjascencies between blocks, +and this graph is progressively transformed in a cactus graph where the nodes +are sets of adjascencies connected together without crossing a block."]] diff --git a/tags/alignment.mdwn b/tags/alignment.mdwn index 795e5919..2bbe4c8b 100644 --- a/tags/alignment.mdwn +++ b/tags/alignment.mdwn @@ -1,4 +1,15 @@ [[!meta title="pages tagged alignment"]] -[[!inline pages="tagged(alignment)" actions="no" archive="yes" -feedshow=10]] +_Work in progress_ + +## LAST + +see [[LAST]] for a detailed bibliography. + +## Cactus + + - 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. + +[[!inline pages="tagged(alignment)" limit=0]] -- 2.47.3