I can recommend MUSTANG: http://p2p.cs.mu.oz.au/mustang/ Web server version is http://p2p.cs.mu.oz.au/mustang/php/ paper is here: http://www.ncbi.nlm.nih.gov/pubmed/16736488?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
Ashley On 05/03/2008, at 6:13 AM, Stephen Graham wrote:
Hi all, I would like to generate a structure-based multiple sequence alignment using 4 structures. I have already generated pairwise alignments for each 'pair' of structures (6 alignments in all). Is there a program out there that can take a number of aligned structures (or even just a number of pairwise sequence alignments) and calculate the 'best' multiple sequence alignment? Please note that there is absolutely no sequence conservation between these structures, making standard sequence-based alignment tools pretty useless. Thanks, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
Ashley Buckle Ph.D NHMRC Senior Research Fellow The Department of Biochemistry and Molecular Biology School of Biomedical Sciences, Faculty of Medicine & Victorian Bioinformatics Consortium (VBC) Monash University, Clayton, Vic 3800 Australia http://www.med.monash.edu.au/biochem/staff/abuckle.html iChat/AIM: blindcaptaincat skype: ashley.buckle Tel: (613) 9902 0269 (office) Tel: (613) 9905 1653 (lab) Fax : (613) 9905 4699
