![]() ![]() sh3_pdb1.template_list: file containing the template associated with every sequence.sh3.html: final alignment colored in function of the CORE index from red (very consistent) to blue (poorly consistent).sh3.aln: final alignment given in ClustalW format.sh3.dnd: guide tree used to assemble the progressive alignment.In this MSA 15 of the columns are similar to the reference HOMSTRAD MSA. Bertrand Dubois fait partie des pionniers qui, en France, ont. Consistency is estimated from a sequence-based T-Coffee library. The Expresso mode produces four different types of output files: De retour Dijon en 2011, il lance lun des premiers coffee shops de la ville : ESPRESSO-T. T_coffee -seq sh3.fasta -mode expresso -pdb_type dn The following command line for Expresso will therefore identify the most suitable PDB templates (X-Ray and NMR structures alike) and will perform a template based sequence alignment: By default Expresso will fetch only XRAY structures, but it is possible to control this behavior via the flag -pdb_type=dn where d for is for diffraction (X-Ray) and n for NMR. Whenever a template is missing, because no structure was similar enough to the considered, proba_pair (the default T-Coffee method for building libraries) is used instead of SAP on every pairwise alignment involving that sequence. Expresso makes an attempt to identify a structure for every sequence and subsequently applies a structural aligner (SAP by default) onto the templates associated with every pair of sequences. By default, PDB structures whose similarity to the original sequence is higher than 30% can be used as a template (this cutoff can be changed -see the troubleshooting section-). In Expresso, the templates are fetched automatically by BLAST. Expresso is the most accurate mode of T-Coffee. ![]()
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