First, it is necessary to put the target TvLDH sequence into the PIR format [74] readable by MODELLER(file `TvLDH.ali').
>P1;TvLDH sequence:TvLDH:::::::0.00: 0.00 MSEAAHVLITGAAGQIGYILSHWIASGELYG-DRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPK AAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPE NFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFKK IGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIHV VEGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG*
The first line contains the sequence code, in the format `>P1;code'. The second line with ten fields separated by colons generally contains information about the structure file, if applicable. Only two of these fields are used for sequences, `sequence' (indicating that the file contains a sequence without known structure) and `TvLDH' (the model file name). The rest of the file contains the sequence of TvLDH, with `*' marking its end. A search for potentially related sequences of known structure can be performed by the SEQUENCE_SEARCH command of MODELLER. The following script uses the query sequence `TvLDH' assigned to the variable ALIGN_CODES from the file `TvLDH.ali' assigned to the variable FILE (file `seqsearch.top').
SET SEARCH_RANDOMIZATIONS = 100 SET FILE = 'TvLDH.ali' SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON
The SEQUENCE_SEARCH command has many options [72], but in this example only SEARCH_RANDOMIZATIONS and DATA_FILE are set to non-default values. SEARCH_RANDOMIZATIONS specifies the number of times the query sequence is randomized during the calculation of the significance score for each sequence-sequence comparison. The higher the number of randomizations, the more accurate the significance score. DATA_FILE = ON triggers creation of an additional summary output file (`seqsearch.dat').