Dear Modeler users!
I have a question about 1st part of basic modeller tutorial. As I understood the* profile.build() method could be useful for scanning *seq_database_file='pdb_95.pir' file where the sequences of the possible templates with known structures are provided against target which are defined further by means of aln.append(file='TvLDH.ali'). Does it possible to use blast search method within the modeller script to create such seq_database_file pir file firstly which will consist of all found pdb's structures with the defined threshold sequence against target sequence (e.g not less as 50% of sequence homology)?
Thanks for help,
James
On 4/16/14, 1:26 AM, James Starlight wrote: > Does it possible to use blast search method within the modeller > script to create such seq_database_file pir file firstly which will > consist of all found pdb's structures with the defined threshold > sequence against target sequence (e.g not less as 50% of sequence > homology)?
You can use any method you like to detect templates (for example, ModPipe employs PSI-BLAST as well as our own methods). You just have to ensure that the files you feed Modeller are in formats (e.g. PIR) that it understands.
Ben Webb, Modeller Caretaker
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James Starlight -
Modeller Caretaker