
                                  twofeat 



Function

   Finds neighbouring pairs of features in sequences

Description

   twofeat reads in the feature tables of sequences and reports
   occurances of pairs of specified features.

   This is intended for use as a simple data-mining tool to enable you to
   look for instances of pairs of features that occur near to each other
   in the same sequence entry.

   For each of the pair of features, you can specify its type name, its
   sense, its score and any tag/value pairs, amongst other things.

   You can then specify the type of relationship that the two features
   should have. You can specify the minimum and maximum distance between
   them. You can specify the type of overlap allowed: Any type of overlap
   or no overlap is allowed, Overlap required, No overlaps are allowed,
   Overlap required but one feature must not be completely within the
   other, Feature A must be completely enclosed within feature B, Feature
   B must be completely enclosed within feature A. You can specify that
   the distance should be measured from the nearest ends of the two
   features, From the left ends, From right ends, From the furthest ends.
   You can specify that the features should be in any sense, in the same
   sense or in opposite senses. You can specify that the features should
   be in any order, Feature A then feature B, Feature B then feature A.

   By default the resulting pairs of features found are then written to a
   report file as a single feature from the first postion of the
   left-most feature to the last position of the right-most feature. You
   can modify the output to report the pairs of features with no changes
   made to them.

Algorithm

For each sequence:
        identify the features that match the criteria for Feature A
        identify the features that match the criteria for Feature B
        compare all pairs of features
        if they satisfy the requirements output them to the report file

Usage

   Here is a sample session with twofeat

   Without the -twoout option the output report contains just one feature
   for every pair of features found.


% twofeat tembl:hsfau 
Finds neighbouring pairs of features in sequences
Type of first feature [*]: polyA_signal
Type of second feature [*]: polyA_site
The minimum distance between the features [0]: 10
The maximum distance between the features [0]: 50
Output report [hsfau.twofeat]: 

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   The -twoout option makes the output report give the pairs of features
   found. The ouput report format type has been changed to display the
   full original pairs of faetures in GFF format.


% twofeat -twoout -rformat gff tembl:hsfau 
Finds neighbouring pairs of features in sequences
Type of first feature [*]: polyA_signal
Type of second feature [*]: polyA_site
The minimum distance between the features [0]: 10
The maximum distance between the features [0]: 50
Output report [hsfau.twofeat]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
   -atype              string     By default every feature in the feature
                                  table is allowed. You can set this to be any
                                  feature type you wish to allow.
                                  See http://www3.ebi.ac.uk/Services/WebFeat/
                                  for a list of the EMBL feature types and see
                                  Appendix A of the Swissprot user manual in
                                  http://www.expasy.ch/txt/userman.txt for a
                                  list of the Swissprot feature types.
                                  The type may be wildcarded by using '*'.
                                  If you wish to allow more than one type,
                                  separate their names with the character '|',
                                  eg:
                                  *UTR | intron
   -btype              string     By default every feature in the feature
                                  table is allowed. You can set this to be any
                                  feature type you wish to allow.
                                  See http://www3.ebi.ac.uk/Services/WebFeat/
                                  for a list of the EMBL feature types and see
                                  Appendix A of the Swissprot user manual in
                                  http://www.expasy.ch/txt/userman.txt for a
                                  list of the Swissprot feature types.
                                  The type may be wildcarded by using '*'.
                                  If you wish to allow more than one type,
                                  separate their names with the character '|',
                                  eg:
                                  *UTR | intron
   -minrange           integer    If this is greater or equal to 'maxrange',
                                  then no min or max range is specified
   -maxrange           integer    If this is less than or equal to 'minrange',
                                  then no min or max range is specified
  [-outfile]           report     Output report file name

   Additional (Optional) qualifiers (* if not always prompted):
   -asource            string     By default any feature source in the feature
                                  table is allowed. You can set this to match
                                  any feature source you wish to allow.
                                  The source name is usually either the name
                                  of the program that detected the feature or
                                  it is the feature table (eg: EMBL) that the
                                  feature came from.
                                  The source may be wildcarded by using '*'.
                                  If you wish to allow more than one source,
                                  separate their names with the character '|',
                                  eg:
                                  gene* | embl
   -asense             menu       By default any feature sense is allowed. You
                                  can set this to match the required sense.
   -aminscore          float      If this is greater than or equal to the
                                  maximum score, then any score is allowed.
   -amaxscore          float      If this is less than or equal to the maximum
                                  score, then any score is permitted.
   -atag               string     Tags are the types of extra values that a
                                  feature may have. For example in the EMBL
                                  feature table, a 'CDS' type of feature may
                                  have the tags '/codon', '/codon_start',
                                  '/db_xref', '/EC_number', '/evidence',
                                  '/exception', '/function', '/gene',
                                  '/label', '/map', '/note', '/number',
                                  '/partial', '/product', '/protein_id',
                                  '/pseudo', '/standard_name', '/translation',
                                  '/transl_except', '/transl_table', or
                                  '/usedin'. Some of these tags also have
                                  values, for example '/gene' can have the
                                  value of the gene name.
                                  By default any feature tag in the feature
                                  table is allowed. You can set this to match
                                  any feature tag you wish to allow.
                                  The tag may be wildcarded by using '*'.
                                  If you wish to allow more than one tag,
                                  separate their names with the character '|',
                                  eg:
                                  gene | label
   -avalue             string     Tag values are the values associated with a
                                  feature tag. Tags are the types of extra
                                  values that a feature may have. For example
                                  in the EMBL feature table, a 'CDS' type of
                                  feature may have the tags '/codon',
                                  '/codon_start', '/db_xref', '/EC_number',
                                  '/evidence', '/exception', '/function',
                                  '/gene', '/label', '/map', '/note',
                                  '/number', '/partial', '/product',
                                  '/protein_id', '/pseudo', '/standard_name',
                                  '/translation', '/transl_except',
                                  '/transl_table', or '/usedin'. Only some of
                                  these tags can have values, for example
                                  '/gene' can have the value of the gene name.
                                  By default any feature tag value in the
                                  feature table is allowed. You can set this
                                  to match any feature tag value you wish to
                                  allow.
                                  The tag value may be wildcarded by using
                                  '*'.
                                  If you wish to allow more than one tag
                                  value, separate their names with the
                                  character '|', eg:
                                  pax* | 10
   -bsource            string     By default any feature source in the feature
                                  table is allowed. You can set this to match
                                  any feature source you wish to allow.
                                  The source name is usually either the name
                                  of the program that detected the feature or
                                  it is the feature table (eg: EMBL) that the
                                  feature came from.
                                  The source may be wildcarded by using '*'.
                                  If you wish to allow more than one source,
                                  separate their names with the character '|',
                                  eg:
                                  gene* | embl
   -bsense             menu       By default any feature sense is allowed. You
                                  can set this to match the required sense.
   -bminscore          float      If this is greater than or equal to the
                                  maximum score, then any score is allowed.
   -bmaxscore          float      If this is less than or equal to the maximum
                                  score, then any score is permitted.
   -btag               string     Tags are the types of extra values that a
                                  feature may have. For example in the EMBL
                                  feature table, a 'CDS' type of feature may
                                  have the tags '/codon', '/codon_start',
                                  '/db_xref', '/EC_number', '/evidence',
                                  '/exception', '/function', '/gene',
                                  '/label', '/map', '/note', '/number',
                                  '/partial', '/product', '/protein_id',
                                  '/pseudo', '/standard_name', '/translation',
                                  '/transl_except', '/transl_table', or
                                  '/usedin'. Some of these tags also have
                                  values, for example '/gene' can have the
                                  value of the gene name.
                                  By default any feature tag in the feature
                                  table is allowed. You can set this to match
                                  any feature tag you wish to allow.
                                  The tag may be wildcarded by using '*'.
                                  If you wish to allow more than one tag,
                                  separate their names with the character '|',
                                  eg:
                                  gene | label
   -bvalue             string     Tag values are the values associated with a
                                  feature tag. Tags are the types of extra
                                  values that a feature may have. For example
                                  in the EMBL feature table, a 'CDS' type of
                                  feature may have the tags '/codon',
                                  '/codon_start', '/db_xref', '/EC_number',
                                  '/evidence', '/exception', '/function',
                                  '/gene', '/label', '/map', '/note',
                                  '/number', '/partial', '/product',
                                  '/protein_id', '/pseudo', '/standard_name',
                                  '/translation', '/transl_except',
                                  '/transl_table', or '/usedin'. Only some of
                                  these tags can have values, for example
                                  '/gene' can have the value of the gene name.
                                  By default any feature tag value in the
                                  feature table is allowed. You can set this
                                  to match any feature tag value you wish to
                                  allow.
                                  The tag value may be wildcarded by using
                                  '*'.
                                  If you wish to allow more than one tag
                                  value, separate their names with the
                                  character '|', eg:
                                  pax* | 10
   -overlap            menu       This allows you to specify the allowed
                                  overlaps of the features A and B.
                                  You can allow any or no overlaps, specify
                                  that they must or must not overlap, that one
                                  must or must not be wholly enclosed within
                                  another feature.
   -rangetype          menu       This allows you to specify the positions
                                  from which the allowed minimum or maximum
                                  distance between the features is measured
   -sense              menu       This allows you to specify the required
                                  sense that the two features must be on. This
                                  is ignored (always 'Any') when looking at
                                  protein sequence features.
   -order              menu       This allows you to specify the required
                                  order of the two features. The order is
                                  measured from the start positions of the
                                  features. This criterion is always applied
                                  despite the specified overlap type required.
   -twoout             toggle     If you set this to be true, then the two
                                  features themselves will be written out. If
                                  it is left as false, then a single feature
                                  will be written out covering the two
                                  features you found.
*  -typeout            string     If you have specified that the pairs of
                                  features that are found should be reported
                                  as one feature in the ouput, then you can
                                  specify the 'type' name of the new feature
                                  here. By default every feature in the
                                  feature table is allowed. See
                                  http://www3.ebi.ac.uk/Services/WebFeat/ for
                                  a list of the EMBL feature types and see
                                  Appendix A of the Swissprot user manual in
                                  http://www.expasy.ch/txt/userman.txt for a
                                  list of the Swissprot feature types. If you
                                  specify an invalid feature type name, then
                                  the default name 'misc_feature' is used.

   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
   -sformat1            string     Input sequence format
   -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
   -rusashow2           boolean    Show the full USA in the report

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write 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. 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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -atype By default every feature in the feature table is allowed. You
   can set this to be any feature type you wish to allow. See
   http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature
   types and see Appendix A of the Swissprot user manual in
   http://www.expasy.ch/txt/userman.txt for a list of the Swissprot
   feature types. The type may be wildcarded by using '*'. If you wish to
   allow more than one type, separate their names with the character '|',
   eg: *UTR | intron Any string is accepted *
   -btype By default every feature in the feature table is allowed. You
   can set this to be any feature type you wish to allow. See
   http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature
   types and see Appendix A of the Swissprot user manual in
   http://www.expasy.ch/txt/userman.txt for a list of the Swissprot
   feature types. The type may be wildcarded by using '*'. If you wish to
   allow more than one type, separate their names with the character '|',
   eg: *UTR | intron Any string is accepted *
   -minrange If this is greater or equal to 'maxrange', then no min or
   max range is specified Any integer value 0
   -maxrange If this is less than or equal to 'minrange', then no min or
   max range is specified Any integer value 0
   [-outfile]
   (Parameter 2) Output report file name Report output file
   Additional (Optional) qualifiers Allowed values Default
   -asource By default any feature source in the feature table is
   allowed. You can set this to match any feature source you wish to
   allow. The source name is usually either the name of the program that
   detected the feature or it is the feature table (eg: EMBL) that the
   feature came from. The source may be wildcarded by using '*'. If you
   wish to allow more than one source, separate their names with the
   character '|', eg: gene* | embl Any string is accepted *
   -asense By default any feature sense is allowed. You can set this to
   match the required sense.
   0 (Any sense)
   + (Forward sense)
   - (Reverse sense)
   0
   -aminscore If this is greater than or equal to the maximum score, then
   any score is allowed. Any numeric value 0.0
   -amaxscore If this is less than or equal to the maximum score, then
   any score is permitted. Any numeric value 0.0
   -atag Tags are the types of extra values that a feature may have. For
   example in the EMBL feature table, a 'CDS' type of feature may have
   the tags '/codon', '/codon_start', '/db_xref', '/EC_number',
   '/evidence', '/exception', '/function', '/gene', '/label', '/map',
   '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo',
   '/standard_name', '/translation', '/transl_except', '/transl_table',
   or '/usedin'. Some of these tags also have values, for example '/gene'
   can have the value of the gene name. By default any feature tag in the
   feature table is allowed. You can set this to match any feature tag
   you wish to allow. The tag may be wildcarded by using '*'. If you wish
   to allow more than one tag, separate their names with the character
   '|', eg: gene | label Any string is accepted *
   -avalue Tag values are the values associated with a feature tag. Tags
   are the types of extra values that a feature may have. For example in
   the EMBL feature table, a 'CDS' type of feature may have the tags
   '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence',
   '/exception', '/function', '/gene', '/label', '/map', '/note',
   '/number', '/partial', '/product', '/protein_id', '/pseudo',
   '/standard_name', '/translation', '/transl_except', '/transl_table',
   or '/usedin'. Only some of these tags can have values, for example
   '/gene' can have the value of the gene name. By default any feature
   tag value in the feature table is allowed. You can set this to match
   any feature tag value you wish to allow. The tag value may be
   wildcarded by using '*'. If you wish to allow more than one tag value,
   separate their names with the character '|', eg: pax* | 10 Any string
   is accepted *
   -bsource By default any feature source in the feature table is
   allowed. You can set this to match any feature source you wish to
   allow. The source name is usually either the name of the program that
   detected the feature or it is the feature table (eg: EMBL) that the
   feature came from. The source may be wildcarded by using '*'. If you
   wish to allow more than one source, separate their names with the
   character '|', eg: gene* | embl Any string is accepted *
   -bsense By default any feature sense is allowed. You can set this to
   match the required sense.
   0 (Any sense)
   + (Forward sense)
   - (Reverse sense)
   0
   -bminscore If this is greater than or equal to the maximum score, then
   any score is allowed. Any numeric value 0.0
   -bmaxscore If this is less than or equal to the maximum score, then
   any score is permitted. Any numeric value 0.0
   -btag Tags are the types of extra values that a feature may have. For
   example in the EMBL feature table, a 'CDS' type of feature may have
   the tags '/codon', '/codon_start', '/db_xref', '/EC_number',
   '/evidence', '/exception', '/function', '/gene', '/label', '/map',
   '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo',
   '/standard_name', '/translation', '/transl_except', '/transl_table',
   or '/usedin'. Some of these tags also have values, for example '/gene'
   can have the value of the gene name. By default any feature tag in the
   feature table is allowed. You can set this to match any feature tag
   you wish to allow. The tag may be wildcarded by using '*'. If you wish
   to allow more than one tag, separate their names with the character
   '|', eg: gene | label Any string is accepted *
   -bvalue Tag values are the values associated with a feature tag. Tags
   are the types of extra values that a feature may have. For example in
   the EMBL feature table, a 'CDS' type of feature may have the tags
   '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence',
   '/exception', '/function', '/gene', '/label', '/map', '/note',
   '/number', '/partial', '/product', '/protein_id', '/pseudo',
   '/standard_name', '/translation', '/transl_except', '/transl_table',
   or '/usedin'. Only some of these tags can have values, for example
   '/gene' can have the value of the gene name. By default any feature
   tag value in the feature table is allowed. You can set this to match
   any feature tag value you wish to allow. The tag value may be
   wildcarded by using '*'. If you wish to allow more than one tag value,
   separate their names with the character '|', eg: pax* | 10 Any string
   is accepted *
   -overlap This allows you to specify the allowed overlaps of the
   features A and B. You can allow any or no overlaps, specify that they
   must or must not overlap, that one must or must not be wholly enclosed
   within another feature.
   A  (Any)
   O  (Overlap required)
   NO (No overlaps are allowed)
   NW (Overlap required but not within)
   AW (A must be all within B)
   BW (B must be all within A)
   A
   -rangetype This allows you to specify the positions from which the
   allowed minimum or maximum distance between the features is measured
   N (From nearest ends)
   L (From left ends)
   R (From right ends)
   F (From furthest ends)
   N
   -sense This allows you to specify the required sense that the two
   features must be on. This is ignored (always 'Any') when looking at
   protein sequence features.
   A (Any sense)
   S (Same sense)
   O (Opposite sense)
   A
   -order This allows you to specify the required order of the two
   features. The order is measured from the start positions of the
   features. This criterion is always applied despite the specified
   overlap type required.
   A  (Any)
   AB (Feature A then feature B)
   BA (Feature B then feature A)
   A
   -twoout If you set this to be true, then the two features themselves
   will be written out. If it is left as false, then a single feature
   will be written out covering the two features you found. Toggle value
   Yes/No No
   -typeout If you have specified that the pairs of features that are
   found should be reported as one feature in the ouput, then you can
   specify the 'type' name of the new feature here. By default every
   feature in the feature table is allowed. See
   http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature
   types and see Appendix A of the Swissprot user manual in
   http://www.expasy.ch/txt/userman.txt for a list of the Swissprot
   feature types. If you specify an invalid feature type name, then the
   default name 'misc_feature' is used. Any string is accepted
   misc_feature
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   twofeat reads any normal sequence USAs.

  Input files for usage example

   'tembl:hsfau' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:hsfau

ID   HSFAU      standard; RNA; HUM; 518 BP.
XX
AC   X65923;
XX
SV   X65923.1
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   23-SEP-1993 (Rel. 37, Last updated, Version 10)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   MEDLINE; 93368957.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8:2537-2546(1993).
XX
DR   SWISS-PROT; P35544; UBIM_HUMAN.
DR   SWISS-PROT; Q05472; RS30_HUMAN.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /chromosome="11q"
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /tissue_type="placenta"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /map="13"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /db_xref="SWISS-PROT:P35544"
FT                   /db_xref="SWISS-PROT:Q05472"
FT                   /gene="fau"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLA
G
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKT
G
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        6
0
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       12
0
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       18
0
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       24
0
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       30
0
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       36
0
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       42
0
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       48
0
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               51
8
//

Output file format

   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, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, regions, seqtable, simple, srs, table, tagseq

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   twofeat outputs a report format file. The default format is table

  Output files for usage example

  File: hsfau.twofeat

########################################
# Program: twofeat
# Rundate: Thu Jul 15 2004 12:00:00
# Report_format: table
# Report_file: hsfau.twofeat
########################################

#=======================================
#
# Sequence: HSFAU     from: 1   to: 518
# HitCount: 1
#=======================================

  Start     End   Score starta   enda startb   endb
    484     509   0.000    484    489    509    509

#---------------------------------------
#---------------------------------------

  Output files for usage example 2

  File: hsfau.twofeat

##gff-version 2.0
##date 2004-07-15
##Type DNA HSFAU
HSFAU   EMBL    polyA_signal    484     489     0.000   +       .       Sequenc
e "HSFAU.6"
HSFAU   EMBL    polyA_site      509     509     0.000   +       .       Sequenc
e "HSFAU.7" ; FeatFlags "0x40"

Data files

   None.

Notes

   It can't find features that are not in the input sequences. It has no
   way of checking whether the input features are correct or not.
   Remember this when you are searching public databases.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   There is a slight memory leak that must be fixed at some time. This
   does no affect the results.

See also

   Program name                      Description
   coderet      Extract CDS, mRNA and translations from feature tables
   extractfeat  Extract features from a sequence
   maskfeat     Mask off features of a sequence
   showfeat     Show features of a sequence

Author(s)

   Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

   Written (2002) - Gary Williams

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
