From: Charles Plessy <charles.plessy@oist.jp>
Date: Tue, 24 Jan 2023 00:35:43 +0000 (+0900)
Subject: Cactus
X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=4714fb72375e4410abdce9561bb97c5d745b00cd;p=setup%2F.git

Cactus
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diff --git a/biblio/21385048.mdwn b/biblio/21385048.mdwn
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+[[!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
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 [[!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]]