algorithm_opt Algorithm options genomic Allows for introns (g) perl (defined $value and $value)? " g=on" : "" 0 datastrand Specifies the read direction of the databse sequences to be used in the search. (datastrand) perl ($value defined) " datastrand=$value" : "" both forward reverse both scoring_opt Scoring options null2 This argument, switch the null2 postprocessing (null2). perl (defined $value && $value ne $vdef)? " null2=$value" : "" on on off full This argument, if set to off, turns off null2 postprocessing. If this parameter is set to on or full, HMMER's null2 score adjustment is intended to correct artifically high scores caused by hits that have large insertions. If this value is set to on while performing an mhsp search that produces only negative hits, the null2 correction will only be performed on the hit with the highest raw score. If this value is set to full while performing an mhsp search that produces only negative hits, the null2 correction will be performed on all of the hits. sam_adjust_score Adjustment of the SAM scoring.(sam_adjust_score) perl ($value)? "" : " sam_adjust_score=0" 2 The only accepted values are 2 (the default) and 0 (no adjustment). If set to 2, BTK computes the score of each hit of a SAM model against a database sequence by subtracting the natural log of the length of the database from the raw score. This works in the same manner as setting adjust_score=2 in the SAM software. SAM software's behaviour when adjust_score=1 is not currently supported by BTK. zscore zscore (z) perl (not $mhsp) perl (defined $value && $value)? " z=on" : "" 0 threshold_opt Treshold options evalue_threshold evalue_threshold (evt) perl ($sort eq "ev") perl (defined $value && $value != $vdef)? " evt=$value" : "" 10.00 evdprob_threshold evdprob_threshold (evdt) perl $sort eq "evd" perl " evdt=$value" 0.0010 pvalue_threshold pvalue_threshold (pvt) perl $sort eq "pv" perl " pvt=$value" 0.0010 zscore_threshold zscore_threshold (zt) perl $sort eq "z" perl " zt=$value" 3.00 threshold Specifies the minimum score of hits to be output.(t) perl (defined $value && $value ne $vdef) ? " t=$value" : "" auto Specifies the minimum score of hits to be output. If the auto option is selected, BTK will calculate a score threshold that is appropriate for the number of alignments and summaries selected. The default is auto. Note that it is rarely necessary to change the value of this parameter. report_opt report or output options 4 format Specifies the output report format. The hmmer output format is the default for hmm searches.(f) perl (defined $value && $value ne $vdef)? " f=$value" : "" h b0 b1 b2 btkml d gff h p p2 p3 r outputmode Specifies the sort order(om) perl (defined $value && $value ne $vdef)? " om=$value" : "" s s u The sorted s option specifies that the queries be returned in the order that they were submitted. The unsorted u option specifies that queries be returned in the order that they were completed. alignments Specifies the number of alignments to be calculated in a search. This value can be set to any non-negative number; a value of zero will cause this report section to be skipped. By default, twenty-five alignments are calculated. (a) perl (defined $value && $value != $vdef)? " a=$value" : "" 25 histogram Creates and displays a score histogram which represents scores .(histogram) perl ($value) ? " histogram=1" : "" 0 Creates and displays a score histogram which represents scores for all documents in the database unless a score threshold is specified. The default is off. Note that this option cannot be used in conjunction with the mhsp=data option. perl (not $mhsp) hist_binsize Specifies the size of the histogram bins.(hist_binsize) perl (defined $value && $value != $vdef) ? " hist_binsize=$value" : "" 1 Specifies the size of the histogram bins when the zscore_histogram or histogram parameter is set to on. Any value greater than 0.01 is allowed. The default value is 1. mhsp Report multiple hits / sequence perl ($value) ? " mhsp=data" : "" 0 Directs BTK to return multiple hits in the same database sequence (data) or to return only a single hit per sequence (no). By allowing more than one hit per database sequence, no potentially important similarity information between the query and a database sequence is omitted when reporting results. This option cannot be used in conjunction with the histogram or the zscore options. The default value is no, meaning that a maximum of one hit can be found for each database sequence. perl (!$histogram || !$zscore) sort Specify the criterion to sort the hits. Default sorting is by E value. (sort) perl (defined $value && $value ne $vdef)? " sort=$value" : "" ev ev evd h l pv z E value - Sorts hits by their E values. The E-value of a hit with score S is the expected number of hits on the database with a score of at least S, taking into account the total size of the database. The closer this number is to zero, the greater the significance of the hit; the closer this value is to the number of sequences in the database, the lower the significance of the hit. EVD probability - Specifies that the hits be sorted by their extreme value distri-bution probabilities. Extreme value distribution (EVD) is the probability of a single score exceeding a given score by chance. The closer this value is to zero, the greater the significance of the hit; the closer it is to one, the lower the significance of the hit. The default value of the EVD threshold is .001. Highscore - Specifies that the results be sorted from the highest to the lowest scores. This score is derived using the matrix associated with the HMM or the matrix selected by the user, depending on the type of query selected. This is the default sorting method if no sort option is specified and the report type is GeneWise; otherwise, hits will be sorted by E value. Loglength - Specifies that the scores be sorted by loglength normalization. P value - Specifies that the scores be sorted by Karlin-Altschul P values. This P value is the probability of seeing at least one occurrence of a score greater than or equal to the given score. Setting a P value threshold will cause all the hits below this threshold to be filtered out. The lower the P value of an alignment, the less likely that the hit is random. The default value for the P value threshold is 0.001. Sequence P value - Specifies that the scores be sorted by their sequence P values. The sequence P value is the probability of a single database sequence having a score greater than or equal to a given score, the sequence P value threshold, considering the lengths of the query and database sequences. The default value for the seq_pvalue is 0.001. Z score - Specifies that the hit be sorted according to their Z score values. The zscore option rescores each hit according to its significance relative to all the other hits retrieved for a given query. Higher scores that occur due to sequence length are normalized. The higher a Z score is, the greater the significance of the hit, the closer it is to zero, the lower the significance of the hit. The default value for the Z score threshold is 3. Z score calculation The Z score is calculated using the following equation: (Normalized Score Mean)/(Standard Deviation). summaries Specifies the number of one-line summaries generated in the result report.. The minimum allowed value is 1. (s) perl (defined $value && $value != $vdef)? " summaries=$value" : "" 250 Specifies the number of one-line summaries generated in the result report.This value can be changed to any positive number. By default, up to 250 one-line summaries are generated. The minimum allowed value is 1. verbosity_opt Verbosity level verbose perl ($warning ne "" || $param ne "" || $timestamp ne "" || $quiet ne "")? " v=" : "" warning outputs all warnings perl ($value)? "w" : "" 0 param outputs the search parameters perl ($value)? "p" : "" 0 timestamp add a timestamp to progress report output. perl ($value)? "t" : "" 0 quiet runs in quiet mode. perl ($value)? "q" : "" 0