Target sequence is read from file FILE.
ALIGN_CODES specifies the code of the target sequence in the FILE file. If only one sequence is in the file, you can use ALIGN_CODES = 'all' to read it without bothering about the actual sequence code.
The database of sequences to be scanned against must be read previously by the READ_SEQUENCE_DB command.
The command uses the dynamic programming method for the best sequence alignment, given the gap creation and extension penalties specified by GAP_PENALTIES_1D and residue type scores read from file RR_FILE. GAP_PENALTIES_1D[1] is a gap creation penalty and GAP_PENALTIES_1D[2] is a gap extension penalty.
The SEARCH_TOP_LIST top hits are written to the log file at the end. The hits are sorted according to the fractional sequence identity score obtained by dividing the number of identical residue pairs by the length of the longer sequence (SEARCH_SORT = 'LONGER') or the shorter sequence (SEARCH_SORT = 'SHORTER').
The final list of hits contains three different significance values:
The calculation of the Z-scores assumes that the random scores are distributed according to the Gaussian distribution, instead of the extreme value distribution [Karlin & Altschul, 1990], which is more correct.
SEARCH_RANDOMIZATIONS specifies how many alignments of the shuffled sequences are done to calculate the significance score for the overall sequence similarity. If 0, the significance is not calculated. If more than 5 randomizations are done, the significance score, not sequence identity, is used for sorting the hit list.
When FAST_SEARCH is on only those sequences that have a database-scan alignment score significance (SIGNI3 in output) above FAST_SEARCH_CUTOFF are used for the ``full'' randomization-based significance calculation. Since the mean and the standard deviation of the distribution obtained by randomizing the two compared sequences are much more appropriate than the corresponding quantities for the target/database comparisons, FAST_SEARCH should be on only when you are in a hurry and the database is large.
If DATA_FILE is on the final results (list of PDB codes with significances, etc.) are also written to a separate file 'seqsearch.dat'.
If OUTPUT is 'LONG', the best alignment for each sequence in the database and its various scores are also written to the log file. If OUTPUT is 'VERY_LONG', individual scores obtained for randomized sequences are also written to the log file (this is almost never needed).
If the selected significance score is larger than SIGNIF_CUTOFF[1] and not more than SIGNIF_CUTOFF[2] units worse than the best hit, all the members of the same group, as defined in SEARCH_GROUP_LIST, are added to the alignment array. Subsequent MALIGN, DENDROGRAM and WRITE_ALIGNMENT can then be used to write out all related PDB chains aligned to the target sequence.
# Example for: SEQUENCE_SEARCH
# This will search the MODELLER database of representative protein chains
# for chains similar to the specified sequence.
SET OUTPUT_CONTROL = 1 1 1 1 1
SET SEARCH_RANDOMIZATIONS = 20 # should use 100 in real life;
SET OFF_DIAGONAL = 9999
SET GAP_PENALTIES_1D = -800 -400
SET CHAINS_LIST = 'very-short-for-test.cod'
READ_SEQUENCE_DB # SEQ_DATABASE_FILE = '$(LIB)/CHAINS_all.seq', ;
# CHAINS_LIST = '$(LIB)/CHAINS_3.0_40_XN.cod', ;
# SEQ_DATABASE_FORMAT = 'PIR'
SEQUENCE_SEARCH FILE = 'toxin.ali', ALIGN_CODES = '1nbt'
MALIGN
WRITE_ALIGNMENT FILE = 'toxin-search.pap', ALIGNMENT_FORMAT = 'PAP'