]> BLIMPS 3.4 score a block or matrix against a database of sequences Wallace & Henikoff J.C. Wallace and S. Henikoff, PATMAT: a searching and extraction program for sequence, pattern and block queries and databases, CABIOS, 8:3, p. 249-254 (1992). Steven Henikoff and Jorja G. Henikoff, Automated assembly of protein blocks for database searching, Nucleic Acids Research, 19:23, p. 6565-6572. (1991) protein:motifs motifs http://bioweb.pasteur.fr/docs/gensoft-aa.html#BLIMPS blimps_matrix blimps_matrix perl "blimps blimps.cs" 0 action perl "SE matrix\\n" 2 blimps.cs sequence_db Sequences database perl "DB /local/gensoft/lib/blimps/db/fasta/$value\\n" uniprot &protdbs; &nucdbs; blimps.cs block_file Block file perl ($value eq "")? "" : "BL $value\\n" To score a block query against a database of sequences, specify the block file name and the sequence database name. The sequence database can be either a protein or DNA database. BLIMPS converts the query block to a position-specific scoring matrix and scores every possible alignment between it and every sequence in the database. If the database is DNA, alignments can be scored in all six translation frames or just the reading frames of the given strand. only one of the block or the matrix files is required perl $matrix_file && $block_file blimps.cs control_parameters Blimps parameters 4 conversion Conversion method for converting a block to a matrix perl "CO $value\\n" 2 4 0 1 2 The field value is a number. The possible values so far are: 0 - Clustering. Same as the original method, but cleaner and without the negative fields in the frequency file. It also does a weighted average of D & N to get B and of E & Q to get Z. If a B or Z is encountered, it is split between D & N or E & Q. 1 - uses patmat's method, needs -1 and -2 in the frequency file - gets weird numbers due to division by zero if there are zeros in the frequency file. 2 - Sequence weighing. The default. The same as clustering except that the weights of the sequences are taken explicitly from the given weights, rather than implicitly from the clustering. perl $block_file && (! $matrix_file) blimps.cs matrix_file A precomputed site specific scoring matrix file (instead of block file) perl ($value eq "")? "" : "MA $value\\n" 4 If you give a block file, Blimps converts it to a position-specific scoring matrix; but you can directly give a matrix file you have one (see conversion parameter). You can produce a matrix file by asking to export matricies to a file, only when action is to score a block query against a database of sequences (matrix). only one of the block or the matrix files is required perl $matrix_file && $block_file perl ( ! $block_file) blimps.cs genetic_code The Genetic code to use (if DNA sequence or database) perl ($value)? "GE $value\\n" : "" 0 4 0 1 2 3 4 5 6 7 8 blimps.cs strands The number of strands to search (if DNA sequence or database) perl ($value && $value != $vdef)? "ST $value\\n" : "" 2 4 If the query is DNA, alignments can be scored in all six translation frames or just the reading frames of the given strand. values allowed: 1 or 2 perl $value != 1 && $value != 2 blimps.cs output_parameters Output parameters 5 outfile Output file filename perl "OU $value\\n" blimps.results 5 blimps.cs error Error level to report at perl "ER $value\\n" 2 1 1 2 3 4 5 Errors of lesser value than the error level are not reported. The program will always handle a fatal error regardless of the error level setting. blimps.cs export_matrix Export matrix (matricies) to this filename perl ($value eq "")? "" : "EX $value\\n" 5 blimps.cs histogram Print the histogram values in the output file perl (! $value)? "" : "HI yes\\n" 0 5 blimps.cs scores The number of scores to report. perl (defined $value)? "NU $value\\n" : "\\n" 0 5 A number less than zero means to report all the scores. A number of zero means to judge the number to report based on the query block or sequence. A number greater than zero is the number to actually report. The default value is zero. blimps.cs repeats Repeats are allowed in the scoring list perl (! $value)? "RE 0\\n" : "" 1 5 blimps.cs config_file blimps.cs