]> BLIMPS 3.4 BLocks IMProved Searcher Wallace, Henikoff motifs blimps blimps perl "blimps blimps.cs " 0 action Action perl "SE $value\\n" block 2 block matrix To score a query sequence against a database of blocks, specify the query sequence file name and the blocks database name. The query can be either a protein or DNA sequence. BLIMPS converts each block in the database to a position-specific scoring matrix and scores every possible alignment between each block and the query. If the query is DNA, alignments can be scored in all six translation frames or just the reading frames of the given strand, depending on the ST field in the configuration file. 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. blimps.cs block_parameters Parameters for sequence against Block db (action=block) perl $action eq "block" 3 blocks_db Blocks database perl "DB /local/gensoft/lib/blimps/db/$value\\n" blocks.dat 3 blocks.dat perl $action eq "block" blimps.cs sequence_file Sequence file filename to score against blocks database perl "SQ $value\\n" 3 8 2 14 4 5 perl $action eq "block" blimps.cs matrix_parameters Parameters for block against sequences db (action=matrix) perl $action eq "matrix" 3 sequence_db Sequences database perl "DB /local/databases/fasta/$value\\n" uniprot 3 &protdbs; &nucdbs; perl $action eq "matrix" blimps.cs block_file Block file filename perl ($value eq "")? "" : "BL $value\\n" 3 only one of the block or the matrix files is required perl $matrix_file && $block_file perl $action eq "matrix" blimps.cs matrix_file A precomputed site specific scoring matrix file perl ($value eq "")? "" : "MA $value\\n" 3 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. 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 $action eq "matrix" blimps.cs control_parameters Control parameters 4 conversion Conversion method for converting a block to a matrix perl "CO $value\\n" 2 4 0 1 2 The field value is a number. The possible values so far are: 0 - Clustering. Same as the original method, but cleaner and without the negative fields in the frequency file. It also does a weighted average of D & N to get B and of E & Q to get Z. If a B or Z is encountered, it is split between D & N or E & Q. 1 - uses patmat's method, needs -1 and -2 in the frequency file - gets weird numbers due to division by zero if there are zeros in the frequency file. 2 - Sequence weighing. The default. The same as clustering except that the weights of the sequences are taken explicitly from the given weights, rather than implicitly from the clustering. blimps.cs genetic_code The Genetic code to use perl ($value)? "GE $value\\n" : "" 0 4 0 1 2 3 4 5 6 7 8 blimps.cs strand both strands to be searched perl (! $value)? "ST 1\\n" : "" 1 4 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 Not allowed for action = block. perl $action eq "matrix" blimps.cs histogram Print the histogram values in the output file perl (! $value)? "" : "HI yes\\n" 0 5 blimps.cs scores_number 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 error_file perl blimps.err 5 config_file blimps.cs