Page de Jean-Michel Richer

Research

Bioinformatics

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Introduction

MALINBA for (Multiple Affine or LINear Block Alignment) is a multiple sequence alignment software based on the extension of the Dynamic Programming framework.

Download

MALINBA is freely available for non commercial purpose.

Linux / Unix : MALINBA v1.0

Some results

Some tests were performed on Balibase 2.0 database of benchmarks. There are two versions of MALINBA:

MALINBA: basic implementation using UPGMA to build a guide-tree with BLOSUM75, gap opening penalty of -11 and gap extension penalty of -1.1
MALINBA_OT: basic implementation using Opal's guide-tree with BLOSUM75, gap opening penalty of -12.9 and gap extension penalty of -1.1

Software	Ref1 SPS	Ref1 CS	Ref2 SPS	Ref2 CS	Ref3 SPS	Ref3 CS	Ref4 SPS	Ref4 CS	Ref5 SPS	Ref5 CS	Average SPS	Average CS	Time (in s)
CLUSTAL	809	707	932	592	723	481	834	623	858	634	831	604	120
TCOFFEE	814	712	928	524	739	480	852	644	943	863	855	644	1653
MALINBA	810	713	917	550	752	523	880	721	973	900	866	681	454
MUSCLE	821	725	935	593	784	543	841	593	972	901	870	671	75
MALINBA_OT	817	723	925	569	776	519	910	780	958	890	877	696	280
OPAL	824	728	934	553	811	550	943	834	955	870	893	707	23,159
MAFFT	829	736	931	525	812	595	947	822	978	911	899	717	98
PROBCONS	849	765	943	623	817	631	939	828	974	892	904	747	711
											Rank

SPS and CS scores on Balibase 2.0 with annotations

Bibliography

Jean-Michel Richer, Vincent Derrien, Jin-Kao Hao, A New Dynamic Programming Algorithm for Multiple Sequence Alignment, (COCOA 07), Xi'an, Shaanxi, China, 12-15 August 2007. LNCS 4616, ISBN 978-3-540-73555-7.

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