2008/6/9 Javier Forment Millet <[EMAIL PROTECTED]>: > Hi, all... > > We are attempting to do a temptative functional annotation for EST-derived > partial ORFs which didn't found an annotated similar sequence in BLAST > searches. Could anyone suggest a software for automated fold recognition by > threading in local computers?
Hi Javier, Not sure if this is really helpful or not, but I have been working on a project called PDBWiki, which maintains an FAQ about protein structures. Although we haven't covered threading explicitly in the FAQ, perhaps the answer to the following question is useful for you: How do I build a homology model? http://pdbwiki.org/index.php/PDB_FAQ#Q:_How_do_I_build_a_homology_model.3F This would probably be your next step after running a threading algorithm to obtain a sequence / structure alignment. However, as Martin pointed out, the first thing to try is probably psi-blast, or a search against a library of HMMs. This is because sometimes you can find very reliable alignments between sequences that have very low sequence identity (and so fail to 'blast'). Cheers, Dan. > Thanks in advance, > > Javier. > > > -- > Javier Forment Millet > Instituto de Biología Celular y Molecular de Plantas (IBMCP) CSIC-UPV > Ciudad Politécnica de la Innovación (CPI) Edificio 8 E, Escalera 7 Puerta E > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > Tlf.:+34-96-3877858 > FAX: +34-96-3877859 > [EMAIL PROTECTED] > > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > -- PDBWiki - http://PDBWiki.Org _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
