a question about SEQUENCE_SEARCH
Hi everyone
I'm currently beginning using MODELLER. I have tried to run the basic example of the tutorial. When I run the SEQUENCE_SEARCH command (using the same script provided in the tutorial) it begin running and writing to the log file, but in certain moment MODELLER stops writing to the log file and never stops running. Those are the last lines written by MODELLER in to my log file
_aln.pos 210 220 230 240 250 260 270 TvLDH TQKVVDVLDHDYVFDTFFKKIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVP 9wgaA E---------------------------FCGGGCQSGACSTDKPCGK-------DAGGRVCTNNYCCS _consrvd * * * * * * *
_aln.pos 280 290 300 310 320 330 TvLDH EGNPYGIK
Can anybody help me?
Thanks in advance
Yunierkis
yunierkis@uclv.edu.cu wrote: > I'm currently beginning using MODELLER. I have tried to run the basic > example of the tutorial. When I run the SEQUENCE_SEARCH command (using the > same script provided in the tutorial) it begin running and writing to the > log file, but in certain moment MODELLER stops writing to the log file and > never stops running.
Be patient. SEQUENCE_SEARCH takes a long time. Just as it says in the tutorial, it takes over an hour (and that's on a 3GHz PC). If you're running on a slow old machine (like an SGI) it could take 10 times as long.
If your search doesn't need to be so rigorous, you could use something like BLAST instead.
Ben Webb, Modeller Caretaker
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yunierkis＠uclv.edu.cu