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- Update pkg-descr PR: 172497 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Feature safe: yes
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SIZE (lagan12.tar.gz) = 112894 | ||
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--- src/glocal/score.cpp.orig 2006-09-15 05:40:19.000000000 +0900 | ||
+++ src/glocal/score.cpp 2012-10-03 00:22:50.000000000 +0900 | ||
@@ -2,7 +2,7 @@ | ||
#include<score.h> | ||
#include<leftinfluence.h> | ||
#include<rightinfluence.h> | ||
-#include<fstream.h> | ||
+#include<fstream> | ||
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extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; | ||
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--- src/utils/Glue.cpp.orig 2006-09-15 05:40:18.000000000 +0900 | ||
+++ src/utils/Glue.cpp 2012-10-03 00:23:38.000000000 +0900 | ||
@@ -6,6 +6,7 @@ | ||
#include <fstream> | ||
#include <iostream> | ||
#include <algorithm> | ||
+#include <cstring> | ||
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#define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" | ||
#define MAX_LINE_LENGTH 1024 |
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The LAGAN Toolkit consists of four components: | ||
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CHAOS, a pairwise local aligner optimized for non-coding, and other | ||
poorly conserved regions of the genome. | ||
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LAGAN, a highly parametrizable pairwise global alignment using local | ||
alignments generated by CHAOS as anchors. | ||
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Multi-LAGAN, a progressive pairwise algorithm to produce multiple | ||
sequence alignments. | ||
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Shuffle-LAGAN, a novel glocal algorithm that is able to find | ||
rearrangements in a global alignment. | ||
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Fast and sensitive multiple alignment of long genomic sequences. BMC | ||
Bioinformatics 2003 4:66. | ||
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LAGAN and Multi-LAGAN: efficient tools for large-scale multiple | ||
alignment of genomic DNA. Genome Res 2003 13(4): 721-31. | ||
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Glocal alignment: finding rearrangements during alignment. Proceedings | ||
of the ISMB 2003, Bioinformatics 19: 54i-62i. | ||
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WWW: http://lagan.stanford.edu/lagan_web/ | ||
The Lagan Tookit is a set of alignment programs for comparative | ||
genomics. The three main components are a pairwise aligner (LAGAN), a | ||
multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All | ||
three are based on the CHAOS local alignment tool and combine speed | ||
(regions up to several megabases can be aligned in minutes) with high | ||
accuracy. The results of the alignment can be visualized using the VISTA | ||
visualization tool. | ||
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WWW: http://lagan.stanford.edu/ |
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