Hello again If you are looking for (known) functional properties you should use multiple alignments tuned so that you align motifs that you know that are related with known functions better than other parts of the protein sequences.
You may know those motifs, because you may know protein domains or motifs that are associated with each function. You may also generate motifs for that purpose, artificially. finally, you may work on the conservation and select the bits of sequence that may have had a common ancestor where that particular function was found. Pedro -- Pedro Fernandes Centro Português de Bioinformática Instituto Gulbenkian de Ciência Apartado 14 2781 OEIRAS PORTUGAL ----------------------------------------------------------- CONFIDENCIAL. Esta mensagem e os ficheiros eventualmente anexos são confidenciais. Se tiver recebido esta mensagem por engano, agradecemos que nos contacte imediatamente por e-mail ou pelo telefone +351 21 4407912 e que elimine a mensagem e ficheiros anexos sem os reproduzir. Quoting Xue Li <[EMAIL PROTECTED]>: > Sorry for the confusion. > > By "Biological distance" I mean functional similarity. > > Thanks. > > Li > > On Wed, Jun 4, 2008 at 3:30 PM, Iddo Friedberg <[EMAIL PROTECTED]> wrote: > > > What is "Biological distance"? > > > > On Wed, Jun 4, 2008 at 9:12 AM, Xue Li <[EMAIL PROTECTED]> wrote: > > > > > Hello all, > > > > > > I have four proteins. 1AAI:A 1RZO:C 1UQ5:A 1UQ4:A > > > > > > Only 1RZO:C, 1UQ5:A and 1UQ4:A have Uniprot accession No. > > > > > > 1RZO:C is P06750 > > > 1UQ5:A and 1UQ4:A are P02879 > > > > > > I am interested in comparing biological distance of 1AAI:A with the other > > > three. Would some one please tell me how to do that? > > > > > > Thanks a lot. > > > > > > -- > > > Xue, Li > > > Bioinformatics and Computational Biology program @ ISU > > > Ames, IA 50010 > > > 515-450-7183 > > > _______________________________________________ > > > BBB mailing list > > > [email protected] > > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > > > > -- > > > > Iddo Friedberg, Ph.D. > > CALIT2, mail code 0440 > > University of California, San Diego > > 9500 Gilman Drive > > La Jolla, CA 92093-0440, USA > > T: +1 (858) 534-0570 > > T: +1 (858) 646-3100 x3516 > > http://iddo-friedberg.org > > _______________________________________________ > > BBB mailing list > > [email protected] > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
