Bio/Tools/Sigcleave.pm

   1 #-----------------------------------------------------------------------------
   2 # PACKAGE : Bio::Tools::Sigcleave
   3 # AUTHOR  : Chris Dagdigian, dag@sonsorol.org
   4 # CREATED : Jan 28 1999
   5 #
   6 # Copyright (c) 1997-9 bioperl, Chris Dagdigian and others. All Rights Reserved.
   7 #           This module is free software; you can redistribute it and/or
   8 #           modify it under the same terms as Perl itself.
   9 #
  10 # _History_
  11 #
  12 # Object framework ripped from Steve Chervits's SeqPattern.pm
  13 #
  14 # Core EGCG Sigcleave emulation from perl code developed by
  15 # Danh Nguyen & Kamalakar Gulukota which itself was based
  16 # loosely on Colgrove's signal.c program.
  17 #
  18 # The overall idea is to replicate the output of the sigcleave
  19 # program which was distributed with the EGCG extension to the GCG sequence
  20 # analysis package. There is also an accessor method for just getting at
  21 # the raw results.
  22 #
  23 #-----------------------------------------------------------------------------
  24
  25 =head1 NAME
  26
  27 Bio::Tools::Sigcleave - Bioperl object for sigcleave analysis
  28
  29 =head1 SYNOPSIS
  30
  31 =head2 Object Creation
  32
  33   use Bio::Tools::Sigcleave ();
  34
  35   # to keep the module backwar compatible, you can pass it a sequence string, but
  36   # there recommended say is to pass it a Seq object
  37
  38   # this works
  39   $seq = "MVLLLILSVLLLKEDVRGSAQSSERRVVAHMPGDIIIGALFSVHHQPTVDKVHERKCGAVREQYGI";
  40   $sig = Bio::Tools::Sigcleave->new(-seq  => $seq,
  41                                                 -type => 'protein',
  42                                                 -threshold=>'3.5',
  43                                                 );
  44   # but you do:
  45   $seqobj = Bio::PrimarySeq->new(-seq => $seq);
  46
  47   $sig = Bio::Tools::Sigcleave->new(-seq  => $seqobj,
  48                                                 -threshold=>'3.5',
  49                                                 );
  50
  51   # now you can detect procaryotic signal sequences as well as eucaryotic
  52   $sig->matrix('eucaryotic'); # or 'procaryotic'
  53
  54
  55 =head2 Object Methods & Accessors
  56
  57   # you can use this method to fine tune the threshod before printing out the results
  58   $sig->result_count:
  59
  60   %raw_results      = $sig->signals;
  61   $formatted_output = $sig->pretty_print;
  62
  63 =head1 DESCRIPTION
  64
  65 "Sigcleave" was a program distributed as part of the free EGCG add-on
  66 to earlier versions of the GCG Sequence Analysis package. A new
  67 implementation of the algorithm is now part of EMBOSS package.
  68
  69 From the EGCG documentation:
  70
  71   SigCleave uses the von Heijne method to locate signal sequences, and
  72   to identify the cleavage site. The method is 95% accurate in
  73   resolving signal sequences from non-signal sequences with a cutoff
  74   score of 3.5, and 75-80% accurate in identifying the cleavage
  75   site. The program reports all hits above a minimum value.
  76
  77 The EGCG Sigcleave program was written by Peter Rice (E-mail:
  78 pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre,
  79 Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SA, UK).
  80
  81 Since EGCG is no longer distributed for the latest versions of GCG,
  82 this code was developed to emulate the output of the original program
  83 as much as possible for those who lost access to sigcleave when
  84 upgrading to newer versions of GCG.
  85
  86 There are 2 accessor methods for this object. "signals" will return a
  87 perl associative array containing the sigcleave scores keyed by amino
  88 acid position.  "pretty_print" returns a formatted string similar to
  89 the output of the original sigcleave utility.
  90
  91 In both cases, the "threshold" setting controls the score reporting
  92 level. If no value for threshold is passed in by the user, the code
  93 defaults to a reporting value of 3.5.
  94
  95 In this implementation the accessor will never return any
  96 score/position pair which does not meet the threshold limit. This is
  97 the slightly different from the behaviour of the 8.1 EGCG sigcleave
  98 program which will report the highest of the under-threshold results
  99 if nothing else is found.
 100
 101
 102 Example of pretty_print output:
 103
 104         SIGCLEAVE of sigtest from: 1 to 146
 105
 106         Report scores over 3.5
 107         Maximum score 4.9 at residue 131
 108
 109          Sequence:  FVILAAMSIQGSA-NLQTQWKSTASLALET
 110                     | (signal)    | (mature peptide)
 111                 118            131
 112
 113          Other entries above 3.5
 114
 115         Maximum score 3.7 at residue 112
 116
 117          Sequence:  CSRQLFGWLFCKV-HPGAIVFVILAAMSIQGSANLQTQWKSTASLALET
 118                    | (signal)    | (mature peptide)
 119                 99            112
 120
 121
 122 =head1 FEEDBACK
 123
 124 When updating and maintaining a module, it helps to know that people
 125 are actually using it. Let us know if you find a bug, think this code
 126 is useful or have any improvements/features to suggest.
 127
 128 =head2 Support
 129
 130 Please direct usage questions or support issues to the mailing list:
 131
 132 I<bioperl-l@bioperl.org>
 133
 134 rather than to the module maintainer directly. Many experienced and
 135 reponsive experts will be able look at the problem and quickly
 136 address it. Please include a thorough description of the problem
 137 with code and data examples if at all possible.
 138
 139 =head2 Reporting Bugs
 140
 141 Report bugs to the Bioperl bug tracking system to help us keep track
 142 the bugs and their resolution. Bug reports can be submitted via the
 143 web:
 144
 145   https://github.com/bioperl/bioperl-live/issues
 146
 147 =head1 AUTHOR
 148
 149 Chris Dagdigian, dag-at-sonsorol.org  & others
 150
 151 =head1 CONTRIBUTORS
 152
 153 Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
 154
 155 =head1 VERSION
 156
 157 Bio::Tools::Sigcleave, $Id$
 158
 159 =head1 COPYRIGHT
 160
 161 Copyright (c) 1999 Chris Dagdigian & others. All Rights Reserved.
 162 This module is free software; you can redistribute it and/or modify it
 163 under the same terms as Perl itself.
 164
 165 =head1 REFERENCES / SEE ALSO
 166
 167 von Heijne G. (1986) "A new method for predicting signal sequences
 168 cleavage sites."  Nucleic Acids Res. 14, 4683-4690.
 169
 170 von Heijne G. (1987) in "Sequence Analysis in Molecular Biology:
 171 Treasure Trove or Trivial Pursuit" (Acad. Press, (1987), 113-117).
 172
 173
 174 =head1 APPENDIX
 175
 176 The following documentation describes the various functions
 177 contained in this module. Some functions are for internal
 178 use and are not meant to be called by the user; they are
 179 preceded by an underscore ("_").
 180
 181 =cut
 182
 183 #
 184 ##
 185 ###
 186 #### END of main POD documentation.
 187 ###
 188 ##
 189 #
 190
 191 package Bio::Tools::Sigcleave;
 192
 193 use Bio::PrimarySeq;
 194
 195 use base qw(Bio::Root::Root);
 196 use strict;
 197 use vars qw ($ID %WeightTable_euc  %WeightTable_pro );
 198 $ID  = 'Bio::Tools::Sigcleave';
 199
 200   %WeightTable_euc = (
 201 #Sample: 161 aligned sequences
 202 # R     -13 -12 -11 -10  -9  -8  -7  -6  -5  -4  -3  -2  -1  +1  +2 Expect
 203  'A' => [16, 13, 14, 15, 20, 18, 18, 17, 25, 15, 47,  6, 80, 18,  6, 14.5],
 204  'C' => [ 3,  6,  9,  7,  9, 14,  6,  8,  5,  6, 19,  3,  9,  8,  3,  4.5],
 205  'D' => [ 0,  0,  0,  0,  0,  0,  0,  0,  5,  3,  0,  5,  0, 10, 11,  8.9],
 206  'E' => [ 0,  0,  0,  1,  0,  0,  0,  0,  3,  7,  0,  7,  0, 13, 14, 10.0],
 207  'F' => [13,  9, 11, 11,  6,  7, 18, 13,  4,  5,  0, 13,  0,  6,  4,  5.6],
 208  'G' => [ 4,  4,  3,  6,  3, 13,  3,  2, 19, 34,  5,  7, 39, 10,  7, 12.1],
 209  'H' => [ 0,  0,  0,  0,  0,  1,  1,  0,  5,  0,  0,  6,  0,  4,  2,  3.4],
 210  'I' => [15, 15,  8,  6, 11,  5,  4,  8,  5,  1, 10,  5,  0,  8,  7,  7.4],
 211  'K' => [ 0,  0,  0,  1,  0,  0,  1,  0,  0,  4,  0,  2,  0, 11,  9, 11.3],
 212  'L' => [71, 68, 72, 79, 78, 45, 64, 49, 10, 23,  8, 20,  1,  8,  4, 12.1],
 213  'M' => [ 0,  3,  7,  4,  1,  6,  2,  2,  0,  0,  0,  1,  0,  1,  2,  2.7],
 214  'N' => [ 0,  1,  0,  1,  1,  0,  0,  0,  3,  3,  0, 10,  0,  4,  7,  7.1],
 215  'P' => [ 2,  0,  2,  0,  0,  4,  1,  8, 20, 14,  0,  1,  3,  0, 22,  7.4],
 216  'Q' => [ 0,  0,  0,  1,  0,  6,  1,  0, 10,  8,  0, 18,  3, 19, 10,  6.3],
 217  'R' => [ 2,  0,  0,  0,  0,  1,  0,  0,  7,  4,  0, 15,  0, 12,  9,  7.6],
 218  'S' => [ 9,  3,  8,  6, 13, 10, 15, 16, 26, 11, 23, 17, 20, 15, 10, 11.4],
 219  'T' => [ 2, 10,  5,  4,  5, 13,  7,  7, 12,  6, 17,  8,  6,  3, 10,  9.7],
 220  'V' => [20, 25, 15, 18, 13, 15, 11, 27,  0, 12, 32,  3,  0,  8, 17, 11.1],
 221  'W' => [ 4,  3,  3,  1,  1,  2,  6,  3,  1,  3,  0,  9,  0,  2,  0,  1.8],
 222  'Y' => [ 0,  1,  4,  0,  0,  1,  3,  1,  1,  2,  0,  5,  0,  1,  7,  5.6]
 223 );
 224
 225   %WeightTable_pro = (
 226 #Sample: 36 aligned sequences
 227 #  R    -13 -12 -11 -10  -9  -8  -7  -6  -5  -4  -3  -2  -1  +1  +2 Expect
 228   'A' => [0,  8,  8,  9,  6,  7,  5,  6,  7,  7, 24,  2, 31, 18,  4,  3.2],
 229   'C' => [1,  0,  0,  1,  1,  0,  0,  1,  1,  0,  0,  0,  0,  0,  0,  1.0],
 230   'D' => [0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  8,  2.0],
 231   'E' => [0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  4,  8,  2.2],
 232   'F' => [2,  4,  3,  4,  1,  1,  8,  0,  4,  1,  0,  7,  0,  1,  0,  1.3],
 233   'G' => [4,  2,  2,  2,  3,  5,  2,  4,  2,  2,  0,  2,  2,  1,  0,  2.7],
 234   'H' => [0,  0,  1,  0,  0,  0,  0,  1,  1,  0,  0,  7,  0,  1,  0,  0.8],
 235   'I' => [3,  1,  5,  1,  5,  0,  1,  3,  0,  0,  0,  0,  0,  0,  2,  1.7],
 236   'K' => [0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  2,  0,  3,  0,  2.5],
 237   'L' => [8, 11,  9,  8,  9, 13,  1,  0,  2,  2,  1,  2,  0,  0,  1,  2.7],
 238   'M' => [0,  2,  1,  1,  3,  2,  3,  0,  1,  2,  0,  4,  0,  0,  1,  0.6],
 239   'N' => [0,  0,  0,  0,  0,  0,  0,  1,  1,  1,  0,  3,  0,  1,  4,  1.6],
 240   'P' => [0,  1,  1,  1,  1,  1,  2,  3,  5,  2,  0,  0,  0,  0,  5,  1.7],
 241   'Q' => [0,  0,  0,  0,  0,  0,  0,  0,  2,  2,  0,  3,  0,  0,  1,  1.4],
 242   'R' => [0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  1.7],
 243   'S' => [1,  0,  1,  4,  4,  1,  5, 15,  5,  8,  5,  2,  2,  0,  0,  2.6],
 244   'T' => [2,  0,  4,  2,  2,  2,  2,  2,  5,  1,  3,  0,  1,  1,  2,  2.2],
 245   'V' => [5,  7,  1,  3,  1,  4,  7,  0,  0,  4,  3,  0,  0,  2,  0,  2.5],
 246   'W' => [0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0.4],
 247   'Y' => [0,  0,  0,  0,  0,  0,  0,  0,  0,  3,  0,  1,  0,  0,  0,  1.3]
 248 );
 249
 250
 251 ##
 252 ## Now we calculate the _real_ values for the weight tables
 253 ##
 254 ##
 255 ## yeah yeah yeah there is lots of math here that gets repeated
 256 ## every single time a sigcleave object gets created. This is
 257 ## a quick hack to make sure that we get the scores as accurate as
 258 ## possible. Need all those significant digits....
 259 ##
 260 ## suggestions for speedup aproaches welcome
 261 ##
 262
 263
 264 foreach my $i (keys %WeightTable_euc) {
 265         my $expected = $WeightTable_euc{$i}[15];
 266         if ($expected > 0) {
 267                 for (my $j=0; $j<16; $j++) {
 268                         if ($WeightTable_euc{$i}[$j] == 0) {
 269                                 $WeightTable_euc{$i}[$j] = 1;
 270                                 if ($j == 10 || $j == 12) {
 271                                         $WeightTable_euc{$i}[$j] = 1.e-10;
 272                                 }
 273                         }
 274                         $WeightTable_euc{$i}[$j] = log($WeightTable_euc{$i}[$j]/$expected);
 275                 }
 276         }
 277 }
 278
 279
 280 foreach my $i (keys %WeightTable_pro) {
 281         my $expected = $WeightTable_pro{$i}[15];
 282         if ($expected > 0) {
 283                 for (my $j=0; $j<16; $j++) {
 284                         if ($WeightTable_pro{$i}[$j] == 0) {
 285                                 $WeightTable_pro{$i}[$j] = 1;
 286                                 if ($j == 10 || $j == 12) {
 287                                         $WeightTable_pro{$i}[$j] = 1.e-10;
 288                                 }
 289                         }
 290                         $WeightTable_pro{$i}[$j] = log($WeightTable_pro{$i}[$j]/$expected);
 291                 }
 292         }
 293 }
 294
 295 #####################################################################################
 296 ##                                 CONSTRUCTOR                                     ##
 297 #####################################################################################
 298
 299
 300 sub new {
 301     my ($class, @args) = @_;
 302
 303     my $self = $class->SUPER::new(@args);
 304     #my $self = Bio::Seq->new(@args);
 305
 306     my ($seq, $threshold, $matrix) = $self->_rearrange([qw(SEQ THRESHOLD MATRIX)],@args);
 307
 308     defined $threshold && $self->threshold($threshold);
 309     $matrix && $self->matrix($matrix);
 310     $seq && $self->seq($seq);
 311
 312     return $self;
 313 }
 314
 315
 316
 317 =head1 threshold
 318
 319  Title     : threshold
 320  Usage     : $value = $self->threshold
 321  Purpose   : Read/write method sigcleave score reporting threshold.
 322  Returns   : float.
 323  Argument  : new value, float
 324  Throws    : on non-number argument
 325  Comments  : defaults to 3.5
 326  See Also   : n/a
 327
 328 =cut
 329
 330 #----------------
 331 sub threshold {
 332 #----------------
 333         my ($self, $value) = @_;
 334         if( defined $value) {
 335                 $self->throw("I need a number, not [$value]")
 336                   if  $value !~ /^[+-]?[\d\.]+$/;
 337                 $self->{'_threshold'} = $value;
 338         }
 339         return $self->{'_threshold'} || 3.5 ;
 340 }
 341
 342 =head1 matrix
 343
 344  Title     : matrix
 345  Usage     : $value = $self->matrix('procaryotic')
 346  Purpose   : Read/write method sigcleave matrix.
 347  Returns   : float.
 348  Argument  : new value: 'eucaryotic' or 'procaryotic'
 349  Throws    : on non-number argument
 350  Comments  : defaults to 3.5
 351  See Also   : n/a
 352
 353 =cut
 354
 355 #----------------
 356 sub matrix {
 357 #----------------
 358         my ($self, $value) = @_;
 359         if( defined $value) {
 360                 $self->throw("I need 'eucaryotic' or 'procaryotic', not [$value]")
 361                   unless  $value eq 'eucaryotic' or $value eq 'procaryotic';
 362                 $self->{'_matrix'} = $value;
 363         }
 364         return $self->{'_matrix'} || 'eucaryotic' ;
 365 }
 366
 367 =head1 seq
 368
 369  Title     : seq
 370  Usage     : $value = $self->seq($seq_object)
 371  Purpose   : set the Seq object to be used
 372  Returns   : Seq object
 373  Argument  : protein sequence or Seq object
 374  See Also   : n/a
 375
 376 =cut
 377
 378 #----------------
 379 sub seq {
 380 #----------------
 381         my ($self, $value) = @_;
 382         if( defined $value) {
 383                 if ($value->isa('Bio::PrimarySeqI')) {
 384                         $self->{'_seq'} = $value;
 385                 } else {
 386                         $self->{'_seq'} = Bio::PrimarySeq->new(-seq => $value,
 387                                                                                                                                 -alphabet => 'protein');
 388                 }
 389         }
 390         return $self->{'_seq'};
 391 }
 392
 393 =head1 _Analyze
 394
 395  Title     : _Analyze
 396  Usage     : N/A This is an internal method. Not meant to be called from outside
 397            : the package
 398            :
 399  Purpose   : calculates sigcleave score and amino acid position for the
 400            : given protein sequence. The score reporting threshold can
 401            : be adjusted by passing in the "threshold" parameter during
 402            : object construction. If no threshold is passed in, the code
 403            : defaults to reporting any scores equal to or above 3.5
 404            :
 405  Returns   : nothing. results are added to the object
 406  Argument  : none.
 407  Throws    : nothing.
 408  Comments  : nothing.
 409 See Also   : n/a
 410
 411 =cut
 412
 413 #----------------
 414 sub _Analyze {
 415 #----------------
 416     my($self) = @_;
 417
 418     my %signals;
 419     my @hitWeight = ();
 420     my @hitsort   = ();
 421     my @hitpos    = ();
 422     my $maxSite   = "";
 423     my $seqPos    = "";
 424     my $istart    = "";
 425     my $iend      = "";
 426     my $icol      = "";
 427     my $i         = "";
 428     my $weight    = "";
 429     my $k         = 0;
 430     my $c         = 0;
 431     my $seqBegin  = 0;
 432     my $pVal      = -13;
 433     my $nVal      = 2;
 434     my $nHits     = 0;
 435     my $seqEnd    = $self->seq->length;
 436     my $pep       = $self->seq->seq;
 437     my $minWeight = $self->threshold;
 438     my $matrix    = $self->matrix;
 439
 440     ## The weight table is keyed by UPPERCASE letters so we uppercase
 441     ## the pep string because we don't want to alter the actual object
 442     ## sequence.
 443
 444     $pep =~ tr/a-z/A-Z/;
 445
 446     for ($seqPos = $seqBegin; $seqPos < $seqEnd; $seqPos++) {
 447                  $istart = (0 > $seqPos + $pVal)? 0 : $seqPos + $pVal;
 448                  $iend = ($seqPos + $nVal - 1 < $seqEnd)? $seqPos + $nVal - 1 : $seqEnd;
 449                  $icol= $iend - $istart + 1;
 450                  $weight = 0.00;
 451                  for ($k=0; $k<$icol; $k++) {
 452                          $c = substr($pep, $istart + $k, 1);
 453
 454                          ## CD: The if(defined) stuff was put in here because Sigcleave.pm
 455                          ## CD: kept getting warnings about undefined vals during 'make test' ...
 456                          if ($matrix eq 'eucaryotic') {
 457                                  $weight += $WeightTable_euc{$c}[$k] if defined $WeightTable_euc{$c}[$k];
 458                          } else {
 459                                  $weight += $WeightTable_pro{$c}[$k] if defined $WeightTable_pro{$c}[$k];
 460                          }
 461                  }
 462                  $signals{$seqPos+1} = sprintf ("%.1f", $weight)        if $weight >= $minWeight;
 463     }
 464     $self->{"_signal_scores"} = { %signals };
 465 }
 466
 467
 468 =head1 signals
 469
 470  Title     : signals
 471  Usage     : %sigcleave_results = $sig->signals;
 472            :
 473  Purpose   : Accessor method for sigcleave results
 474            :
 475  Returns   : Associative array. The key value represents the amino acid position
 476            : and the value represents the score. Only scores that
 477            : are greater than or equal to the THRESHOLD value are reported.
 478            :
 479  Argument  : none.
 480  Throws    : none.
 481  Comments  : none.
 482 See Also   : THRESHOLD
 483
 484 =cut
 485
 486 #----------------
 487 sub signals {
 488 #----------------
 489         my $self = shift;
 490         my %results;
 491         my $position;
 492
 493         # do the calculations
 494         $self->_Analyze;
 495
 496         foreach $position ( sort keys %{ $self->{'_signal_scores'} } ) {
 497                 $results{$position} = $self->{'_signal_scores'}{$position};
 498         }
 499         return %results;
 500 }
 501
 502
 503 =head1 result_count
 504
 505  Title     : result_count
 506  Usage     : $count = $sig->result_count;
 507            :
 508  Purpose   : Accessor method for sigcleave results
 509            :
 510  Returns   : Integer, number of results above the threshold
 511            :
 512  Argument  : none.
 513  Throws    : none.
 514  Comments  : none.
 515
 516 See Also   : THRESHOLD
 517
 518 =cut
 519
 520 #----------------
 521 sub result_count {
 522 #----------------
 523         my $self = shift;
 524         $self->_Analyze;
 525         return keys %{ $self->{'_signal_scores'} };
 526 }
 527
 528
 529 =head1 pretty_print
 530
 531  Title     : pretty_print
 532  Usage     : $output = $sig->pretty_print;
 533            : print $sig->pretty_print;
 534            :
 535  Purpose   : Emulates the output of the EGCG Sigcleave
 536            : utility.
 537            :
 538  Returns   : A formatted string.
 539  Argument  : none.
 540  Throws    : none.
 541  Comments  : none.
 542 See Also   : n/a
 543
 544 =cut
 545
 546 #----------------
 547 sub pretty_print {
 548 #----------------
 549     my $self = shift;
 550     my $pos;
 551     my $output;
 552     my $cnt = 1;
 553     my %results  = $self->signals;
 554     my @hits     = keys %results;
 555     my $hitcount = $#hits; $hitcount++;
 556     my $thresh   = $self->threshold;
 557     my $seqlen   = $self->seq->length || 0;
 558     my $name     = $self->seq->id || 'NONAME';
 559     my $pep      = $self->seq->seq;
 560     $pep      =~ tr/a-z/A-Z/;
 561
 562     $output = "SIGCLEAVE of $name from: 1 to $seqlen\n\n";
 563
 564     if ($hitcount > 0) {
 565                  $output .= "Report scores over $thresh\n";
 566                  foreach $pos ((sort { $results{$b} cmp $results{$a} } keys %results)) {
 567                          my $start = $pos - 15;
 568                          $start = 1 if $start < 1;
 569                          my $sig = substr($pep,$start -1,$pos-$start );
 570
 571                          $output .= sprintf ("Maximum score %1.1f at residue %3d\n",$results{$pos},$pos);
 572                          $output .= "\n";
 573                          $output .= " Sequence:  ";
 574                          $output .= $sig;
 575                          $output .= "-" x (15- length($sig));
 576                          $output .= "-";
 577                          $output .= substr($pep,$pos-1,50);
 578                          $output .= "\n";
 579                          $output .= " " x 12;
 580                          $output .= "| \(signal\)      | \(mature peptide\)\n";
 581                          $output .= sprintf("          %3d             %3d\n\n",$start,$pos);
 582
 583                          if (($hitcount > 1) && ($cnt == 1)) {
 584                                  $output .= " Other entries above $thresh\n\n";
 585                          }
 586                          $cnt++;
 587                  }
 588     }
 589     $output;
 590 }
 591
 592
 593 1;
 594 __END__
 595
 596
 597 #########################################################################
 598 #  End of class
 599 #########################################################################