|   | antigenic | 
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Antigenic predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. This method is based on a single parameter and thus very simple to use.
Analysis of data from experimentally determined antigenic sites on proteins has revealed that the hydrophobic residues Cys, Leu and Val, if they occur on the surface of a protein, are more likely to be a part of antigenic sites. The method of Kolaskar and Tongaonkar to predict antigenic determinants in proteins is semi-empirical and makes use of physicochemical properties of amino acid residues and their frequencies of occurrence in experimentally known segmental epitopes.
| % antigenic Find antigenic sites in proteins Input protein sequence(s): tsw:actb1_takru Minimum length of antigenic region [6]: Output report [actb1_takru.antigenic]: | 
Go to the input files for this example
Go to the output files for this example
Example 2
By using the '-rformat gff' qualifier, a GFF file of the predicted regions can be produced.
| % antigenic -rformat gff Find antigenic sites in proteins Input protein sequence(s): tsw:actb1_takru Minimum length of antigenic region [6]: Output report [actb1_takru.antigenic]: | 
Go to the output files for this example
| 
Find antigenic sites in proteins
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
   -minlen             integer    [6] Minimum length of antigenic region
                                  (Integer from 1 to 50)
  [-outfile]           report     [*.antigenic] Output report file name
                                  (default -rformat motif)
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name
   "-outfile" associated qualifiers
   -rformat2           string     Report format
   -rname2             string     Base file name
   -rextension2        string     File name extension
   -rdirectory2        string     Output directory
   -raccshow2          boolean    Show accession number in the report
   -rdesshow2          boolean    Show description in the report
   -rscoreshow2        boolean    Show the score in the report
   -rstrandshow2       boolean    Show the nucleotide strand in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit
 | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) | seqall | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| -minlen | integer | Minimum length of antigenic region | Integer from 1 to 50 | 6 | 
| [-outfile] (Parameter 2) | report | Output report file name | (default -rformat motif) | <*>.antigenic | 
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0 | 
| -send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0 | 
| -sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N | 
| -sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | 
| -snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N | 
| -sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N | 
| -slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N | 
| -supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N | 
| -scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N | 
| -squick1 -squick_sequence | boolean | Read id and sequence only | Boolean value Yes/No | N | 
| -sformat1 -sformat_sequence | string | Input sequence format | Any string | |
| -iquery1 -iquery_sequence | string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0 | 
| -sdbname1 -sdbname_sequence | string | Database name | Any string | |
| -sid1 -sid_sequence | string | Entryname | Any string | |
| -ufo1 -ufo_sequence | string | UFO features | Any string | |
| -fformat1 -fformat_sequence | string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence | string | Features file name | Any string | |
| "-outfile" associated report qualifiers | ||||
| -rformat2 -rformat_outfile | string | Report format | Any string | motif | 
| -rname2 -rname_outfile | string | Base file name | Any string | |
| -rextension2 -rextension_outfile | string | File name extension | Any string | |
| -rdirectory2 -rdirectory_outfile | string | Output directory | Any string | |
| -raccshow2 -raccshow_outfile | boolean | Show accession number in the report | Boolean value Yes/No | N | 
| -rdesshow2 -rdesshow_outfile | boolean | Show description in the report | Boolean value Yes/No | N | 
| -rscoreshow2 -rscoreshow_outfile | boolean | Show the score in the report | Boolean value Yes/No | Y | 
| -rstrandshow2 -rstrandshow_outfile | boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y | 
| -rusashow2 -rusashow_outfile | boolean | Show the full USA in the report | Boolean value Yes/No | N | 
| -rmaxall2 -rmaxall_outfile | integer | Maximum total hits to report | Any integer value | 0 | 
| -rmaxseq2 -rmaxseq_outfile | integer | Maximum hits to report for one sequence | Any integer value | 0 | 
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | 
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | 
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | 
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | 
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | 
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | 
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | 
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | 
| -error | boolean | Report errors | Boolean value Yes/No | Y | 
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | 
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | 
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | 
| 
ID   ACTB1_TAKRU             Reviewed;         375 AA.
AC   P68142; P53484;
DT   25-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT   25-OCT-2004, sequence version 1.
DT   16-MAY-2012, entry version 49.
DE   RecName: Full=Actin, cytoplasmic 1;
DE   AltName: Full=Beta-actin A;
DE   Contains:
DE     RecName: Full=Actin, cytoplasmic 1, N-terminally processed;
GN   Name=actba;
OS   Takifugu rubripes (Japanese pufferfish) (Fugu rubripes).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei;
OC   Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes;
OC   Tetradontoidea; Tetraodontidae; Takifugu.
OX   NCBI_TaxID=31033;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND TISSUE SPECIFICITY.
RX   MEDLINE=96275651; PubMed=8683572; DOI=10.1006/jmbi.1996.0347;
RA   Venkatesh B., Tay B.H., Elgar G., Brenner S.;
RT   "Isolation, characterization and evolution of nine pufferfish (Fugu
RT   rubripes) actin genes.";
RL   J. Mol. Biol. 259:655-665(1996).
CC   -!- FUNCTION: Actins are highly conserved proteins that are involved
CC       in various types of cell motility and are ubiquitously expressed
CC       in all eukaryotic cells.
CC   -!- SUBUNIT: Polymerization of globular actin (G-actin) leads to a
CC       structural filament (F-actin) in the form of a two-stranded helix.
CC       Each actin can bind to 4 others.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton.
CC   -!- TISSUE SPECIFICITY: Widely distributed. Not expressed in skeletal
CC       muscle.
CC   -!- PTM: Oxidation of Met-44 by MICALs (MICAL1, MICAL2 or MICAL3) to
CC       form methionine sulfoxide promotes actin filament
CC       depolymerization. Methionine sulfoxide is produced
CC       stereospecifically, but it is not known whether the (S)-S-oxide or
CC       the (R)-S-oxide is produced (By similarity).
CC   -!- MISCELLANEOUS: In vertebrates 3 main groups of actin isoforms,
CC       alpha, beta and gamma have been identified. The alpha actins are
CC       found in muscle tissues and are a major constituent of the
CC       contractile apparatus. The beta and gamma actins coexist in most
CC       cell types as components of the cytoskeleton and as mediators of
CC       internal cell motility.
CC   -!- MISCELLANEOUS: There are three different beta-cytoplasmic actins
CC       in Fugu rubripes.
CC   -!- SIMILARITY: Belongs to the actin family.
CC   -----------------------------------------------------------------------
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DR   EMBL; U37499; AAC59889.1; -; Genomic_DNA.
DR   PIR; S71124; S71124.
DR   ProteinModelPortal; P68142; -.
DR   SMR; P68142; 2-375.
DR   Ensembl; ENSTRUT00000013141; ENSTRUP00000013080; ENSTRUG00000005447.
DR   eggNOG; COG5277; -.
DR   GeneTree; ENSGT00630000089629; -.
DR   InParanoid; P68142; -.
DR   OMA; IKNLMER; -.
DR   OrthoDB; EOG41JZC9; -.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-KW.
DR   GO; GO:0005856; C:cytoskeleton; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   InterPro; IPR004000; Actin-like.
DR   InterPro; IPR020902; Actin/actin-like_CS.
DR   InterPro; IPR004001; Actin_CS.
DR   PANTHER; PTHR11937; Actin_like; 1.
DR   Pfam; PF00022; Actin; 1.
DR   PRINTS; PR00190; ACTIN.
DR   SMART; SM00268; ACTIN; 1.
DR   PROSITE; PS00406; ACTINS_1; 1.
DR   PROSITE; PS00432; ACTINS_2; 1.
DR   PROSITE; PS01132; ACTINS_ACT_LIKE; 1.
PE   2: Evidence at transcript level;
KW   Acetylation; ATP-binding; Complete proteome; Cytoplasm; Cytoskeleton;
KW   Methylation; Nucleotide-binding; Oxidation; Reference proteome.
FT   CHAIN         1    375       Actin, cytoplasmic 1.
FT                                /FTId=PRO_0000367094.
FT   INIT_MET      1      1       Removed; alternate (By similarity).
FT   CHAIN         2    375       Actin, cytoplasmic 1, N-terminally
FT                                processed.
FT                                /FTId=PRO_0000000809.
FT   MOD_RES       1      1       N-acetylmethionine; in Actin, cytoplasmic
FT                                1; alternate (By similarity).
FT   MOD_RES       2      2       N-acetylglutamate; in Actin, cytoplasmic
FT                                1, N-terminally processed (By
FT                                similarity).
FT   MOD_RES      44     44       Methionine sulfoxide (By similarity).
FT   MOD_RES      73     73       Tele-methylhistidine (By similarity).
SQ   SEQUENCE   375 AA;  41767 MW;  9C505616D33E9495 CRC64;
     MEDEIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS
     KRGILTLKYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT
     QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT HTVPIYEGYA LPHAILRLDL
     AGRDLTDYLM KILTERGYSF TTTAEREIVR DIKEKLCYVA LDFEQEMGTA ASSSSLEKSY
     ELPDGQVITI GNERFRCPEA LFQPSFLGME SCGIHETTYN SIMKCDVDIR KDLYANTVLS
     GGTTMYPGIA DRMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWISKQ
     EYDESGPSIV HRKCF
//
 | 
The output is a standard EMBOSS report file.
The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.
By default antigenic writes a 'motif' report file.
| 
########################################
# Program: antigenic
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: antigenic
#    -sequence tsw:actb1_takru
# Report_format: motif
# Report_file: actb1_takru.antigenic
########################################
#=======================================
#
# Sequence: ACTB1_TAKRU     from: 1   to: 375
# HitCount: 18
#=======================================
Max_score_pos at "*"
(1) Score 1.207 length 9 at residues 214->222
               *
 Sequence: EKLCYVALD
           |       |
         214       222
 Max_score_pos: 218
(2) Score 1.187 length 15 at residues 131->145
                 *
 Sequence: AMYVAIQAVLSLYAS
           |             |
         131             145
 Max_score_pos: 137
(3) Score 1.166 length 8 at residues 5->12
              *
 Sequence: IAALVVDN
           |      |
           5      12
 Max_score_pos: 8
(4) Score 1.164 length 12 at residues 27->38
                *
 Sequence: PRAVFPSIVGRP
           |          |
          27          38
 Max_score_pos: 32
(5) Score 1.136 length 24 at residues 160->183
                        *
 Sequence: THTVPIYEGYALPHAILRLDLAGR
           |                      |
         160                      183
  [Part of this file has been deleted for brevity]
                        *
 Sequence: SSSSLEKSYELPDGQVITI
           |                 |
         232                 250
 Max_score_pos: 245
(13) Score 1.083 length 6 at residues 327->332
              *
 Sequence: IKIIAP
           |    |
         327    332
 Max_score_pos: 330
(14) Score 1.074 length 7 at residues 317->323
              *
 Sequence: ITALAPS
           |     |
         317     323
 Max_score_pos: 320
(15) Score 1.068 length 7 at residues 186->192
                *
 Sequence: TDYLMKI
           |     |
         186     192
 Max_score_pos: 191
(16) Score 1.066 length 7 at residues 40->46
              *
 Sequence: HQGVMVG
           |     |
          40     46
 Max_score_pos: 43
(17) Score 1.045 length 7 at residues 269->275
           *
 Sequence: MESCGIH
           |     |
         269     275
 Max_score_pos: 269
(18) Score 1.034 length 7 at residues 51->57
            *
 Sequence: DSYVGDE
           |     |
          51     57
 Max_score_pos: 52
#---------------------------------------
#---------------------------------------
 | 
| ##gff-version 3 ##sequence-region ACTB1_TAKRU 1 375 #!Date 2013-07-15 #!Type Protein #!Source-version EMBOSS 6.6.0.0 ACTB1_TAKRU antigenic epitope 214 222 1.207 . . ID=ACTB1_TAKRU.1;note=*pos 218 ACTB1_TAKRU antigenic epitope 131 145 1.187 . . ID=ACTB1_TAKRU.2;note=*pos 137 ACTB1_TAKRU antigenic epitope 5 12 1.166 . . ID=ACTB1_TAKRU.3;note=*pos 8 ACTB1_TAKRU antigenic epitope 27 38 1.164 . . ID=ACTB1_TAKRU.4;note=*pos 32 ACTB1_TAKRU antigenic epitope 160 183 1.136 . . ID=ACTB1_TAKRU.5;note=*pos 173 ACTB1_TAKRU antigenic epitope 367 372 1.135 . . ID=ACTB1_TAKRU.6;note=*pos 372 ACTB1_TAKRU antigenic epitope 93 108 1.116 . . ID=ACTB1_TAKRU.7;note=*pos 103 ACTB1_TAKRU antigenic epitope 295 301 1.113 . . ID=ACTB1_TAKRU.8;note=*pos 296 ACTB1_TAKRU antigenic epitope 256 266 1.11 . . ID=ACTB1_TAKRU.9;note=*pos 264 ACTB1_TAKRU antigenic epitope 336 352 1.107 . . ID=ACTB1_TAKRU.10;note=*pos 347 ACTB1_TAKRU antigenic epitope 62 76 1.102 . . ID=ACTB1_TAKRU.11;note=*pos 68 ACTB1_TAKRU antigenic epitope 232 250 1.086 . . ID=ACTB1_TAKRU.12;note=*pos 245 ACTB1_TAKRU antigenic epitope 327 332 1.083 . . ID=ACTB1_TAKRU.13;note=*pos 330 ACTB1_TAKRU antigenic epitope 317 323 1.074 . . ID=ACTB1_TAKRU.14;note=*pos 320 ACTB1_TAKRU antigenic epitope 186 192 1.068 . . ID=ACTB1_TAKRU.15;note=*pos 191 ACTB1_TAKRU antigenic epitope 40 46 1.066 . . ID=ACTB1_TAKRU.16;note=*pos 43 ACTB1_TAKRU antigenic epitope 269 275 1.045 . . ID=ACTB1_TAKRU.17;note=*pos 269 ACTB1_TAKRU antigenic epitope 51 57 1.034 . . ID=ACTB1_TAKRU.18;note=*pos 52 | 
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
Here is the default Eantigenic.dat file:
# Kolaskar AS and Tongaonkar PC (1990) FEBS Letters 276:172-174 # "A semi-emipirical method for prediction of antigenic determinants # on protein antigens" # # TABLE 1: Occurrence of amino acids in epitopes, proteins and on the surface, # and their antigenic propensity, A(p), values # # 169 antigenic determinants experimentally determined. Selected those 156 # which have less than 20 amino acids per determinant (total 2066 residues). # Calculated f(Ag) as frequency of occurrence of each residue in antigenic # determinants [f(Ag) = Epitope_occurrence/2066]. # # Used Hydrophilicity, Accessibility and Flexibility of Parker JMR, Guo D, # Hodges, RS (1986) Biochemistry 25:5425-5432. In a given protein, calculated # average for each 7-mer and assigned values to central residue of 7-mer. # Residue considered to be on the surface if any of the 7-mer values was above # the average for the protein. Used these results to get f(s) frequency of # occurrence of amino acids at the surface. # # Original table covers the 20 naturally occurring amino acids. # Values for B, Z, X use weighted averages from Edayhoff.dat # and are ignored when calculating totals # # Antigenic propensity column A(p) = f(Ag)/f(s) # # f(s) values below were back-calculated from the table in the paper # # Prediction algorithm: # # 1. calculate average propensity for each overlapping 7-mer, assign to # central residue (i+3) # # 2. calculate average for whole protein A(p)av # # 3. (a) if average for whole protein >= 1.0 then all residues having # >= 1.0 are potentially antigenic. # (b) if average for whole protein < 1.0 then all residues having # > average for whole protein (??? paper has a mangled # formula here :-) are potentially antigenic. # # 4. Find 6-mers where all residues are selected by step 3 above # # Antigenic Surface Antigenic # Amino -- Occurrence of amino acids in -- frequency frequency propensity # Acid Epitopes Surface Protein f(Ag) f(s) A(p) A 135 328 524 0.065 0.061 1.064 B 107 334 410 0.052 0.062 0.827 C 53 97 186 0.026 0.018 1.412 D 118 352 414 0.057 0.066 0.866 E 132 401 499 0.064 0.075 0.851 F 76 180 365 0.037 0.034 1.091 G 116 343 487 0.056 0.064 0.874 H 59 138 191 0.029 0.026 1.105 I 86 193 437 0.042 0.036 1.152 K 158 439 523 0.076 0.082 0.930 L 149 308 684 0.072 0.058 1.250 M 23 72 152 0.011 0.013 0.826 N 94 313 407 0.045 0.058 0.776 P 135 328 411 0.065 0.061 1.064 Q 99 252 332 0.048 0.047 1.015 R 106 314 394 0.051 0.058 0.873 S 168 429 553 0.081 0.080 1.012 T 141 401 522 0.068 0.075 0.909 V 128 239 515 0.062 0.045 1.383 W 19 55 103 0.009 0.010 0.893 X 118 306 453 0.057 0.057 1.025 Y 71 158 245 0.034 0.029 1.161 Z 119 342 433 0.058 0.064 0.916 Total 2066 5340 7944
Application of this method to a large number of proteins has shown that their method can predict antigenic determinants with about 75% accuracy which is better than most of the known methods.
| Program name | Description | 
|---|---|
| epestfind | Find PEST motifs as potential proteolytic cleavage sites | 
| fuzzpro | Search for patterns in protein sequences | 
| fuzztran | Search for patterns in protein sequences (translated) | 
| patmatdb | Search protein sequences with a sequence motif | 
| patmatmotifs | Scan a protein sequence with motifs from the PROSITE database | 
| preg | Regular expression search of protein sequence(s) | 
| pscan | Scan protein sequence(s) with fingerprints from the PRINTS database | 
| sigcleave | Report on signal cleavage sites in a protein sequence | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Original program "ANTIGENIC" by Peter Rice (EGCG 1991)
Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Completed 9th March 1999