Thanks, I was really looking for these 3 ones!! I'm very knew in Bioinformatics, so can I ask if there is others algorithms that are really used? I only know these 3 ones (SW, NW and HMM)!!
Thanks Anderson Moura - Brazil -----Mensagem original----- De: Sylvain Foisy [mailto:[EMAIL PROTECTED] Enviada em: quinta-feira, 9 de março de 2006 14:46 Para: Anderson Moura da Silva Cc: [EMAIL PROTECTED] Assunto: Re: [Biojava-l] Alignmente algorithms implemented by BioJava Hi there, The CVS code in BioJava contains the necessary classes to perform both Smith-Waterman and Needleman-Wunch pairwise alignments. Just have a look at the Javadocs for instructions. The preferred way around here is based around using HMMs to perform the alignments; for this look at the Cookbook section of the BioJava's new website for ways to do that (http://biojava.open-bio.org). As far as MSA are concerned, I don't think that there is anything to do that in BJ. You could call clustal from within your program and use BJ's MSA parsing classes to do your stuff. Hope this helps Sylvain On 3/9/06 11:59 AM, "[NAME]" <[ADDRESS]> wrote: > Hi, > > Can somebody tell me what algorithms Biojava uses to make local alignments and > multiples alignments? > I'm Serching it on the Documentation but I have not found it? > > Where could I find it? I'm working on a Java Environment for Analysis and > Alignment of Sequences! > > Thanks, > Anderson Moura - Brazil > > > Esta mensagem, incluindo seus anexos, pode conter informações privilegiadas > e/ou de caráter confidencial, não podendo ser retransmitida sem autorização do > remetente. Se você não é o destinatário ou pessoa autorizada a recebê-la, > informamos que o seu uso, divulgação, cópia ou arquivamento são proibidos. > Portanto, se você recebeu esta mensagem por engano, por favor, nos informe > respondendo imediatamente a este e-mail e em seguida apague-a. > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > ================================================================== Sylvain Foisy, Ph. D. Directeur - operations / Project Manager BioneQ - Reseau quebecois de bio-informatique U. de Montreal / Genome-Quebec Adresse postale: Departement de biochimie Pavillon principal 2900, boul. Édouard-Montpetit Montréal (Québec) H3T 1J4 Tel: (514) 343-6111 x.2545 Fax: (514) 343-7759 Courriel: [EMAIL PROTECTED] ================================================================== _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
