
                                 maskfeat 



Function

   Mask off features of a sequence

Description

   maskfeat reads in a sequence with its associated features. The
   features can be found in the annotation of the sequence if it is in a
   format such as EMBL or SWISSPROT which includes features in the
   annotation, or they may be supplied explicitly in a GFF file by using
   the command-lin option '-gff filename'.

   The feature table is then searched for features whose type matches the
   specified feature type to be masked. By default, the type is 'repeat*'
   (i.e. any type whose name starts with 'repeat'). You can specify the
   name of any other type of feature, or features that you wish to mask.
   If you wish to specify more than one type of feature, separate their
   names with spaces or commas. The names of the types of feature to be
   found may be wild-carded with asterisks '*' to find gruops of feature
   types sharing a common part of their names.

   If you are unsure of the names of feature types in use, please consult
   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 any features matching the specified names of feature types are
   found, then those regions of the sequence will be masked out by
   replacing that part of the sequence by masking characters. The default
   masking characters are 'X' for a protein sequence and 'N' for a
   nucleic acid sequence, although you can specify your own masking
   character, if required.

   Some non-EMBOSS programs (for example FASTA) are capable of treating
   lower-case regions as if they are masked. maskfeat can mask a region
   to lower-case instead of replacing the sequence with 'N's or 'X's if
   you use the qualifier '-tolower' or use a space character as the
   masking character.

Usage

   Here is a sample session with maskfeat

   Mask out a feature whose type is "repeat_region" from position 2331 to
   2356:


% maskfeat tembl:ab000360 
Mask off features of a sequence.
Output sequence [ab000360.fasta]: 

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

   Example 2

   Change to lower-case a feature whose type is "repeat_region" from
   position 2331 to 2356. Note that '-supper' is used to make the whole
   sequence upper-case before the lower-case masking:


% maskfeat tembl:ab000360 -tolower -supper 
Mask off features of a sequence.
Output sequence [ab000360.fasta]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outseq]            seqout     Output sequence USA

   Additional (Optional) qualifiers (* if not always prompted):
   -type               string     By default any feature in the feature table
                                  with a type starting 'repeat' is masked. You
                                  can set this to be any feature type you
                                  wish to mask.
                                  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 mask more than one type,
                                  separate their names with spaces or commas,
                                  eg:
                                  *UTR repeat*
   -tolower            toggle     The region can be 'masked' by converting the
                                  sequence characters to lower-case, some
                                  non-EMBOSS programs e.g. fasta can interpret
                                  this as a masked region. The sequence is
                                  unchanged apart from the case change. You
                                  might like to ensure that the whole sequence
                                  is in upper-case before masking the
                                  specified regions to lower-case by using the
                                  '-supper' flag.
*  -maskchar           string     Character to use when masking.
                                  Default is 'X' for protein sequences, 'N'
                                  for nucleic sequences.
                                  If the mask character is set to be the SPACE
                                  character or a null character, then the
                                  sequence is 'masked' by changing it to
                                  lower-case, just as with the '-lowercase'
                                  flag.

   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

   "-outseq" associated qualifiers
   -osformat2           string     Output seq format
   -osextension2        string     File name extension
   -osname2             string     Base file name
   -osdirectory2        string     Output directory
   -osdbname2           string     Database name to add
   -ossingle2           boolean    Separate file for each entry
   -oufo2               string     UFO features
   -offormat2           string     Features format
   -ofname2             string     Features file name
   -ofdirectory2        string     Output directory

   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
   [-outseq]
   (Parameter 2) Output sequence USA Writeable sequence <sequence>.format
   Additional (Optional) qualifiers Allowed values Default
   -type By default any feature in the feature table with a type starting
   'repeat' is masked. You can set this to be any feature type you wish
   to mask. 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
   mask more than one type, separate their names with spaces or commas,
   eg: *UTR repeat* Any string is accepted repeat*
   -tolower The region can be 'masked' by converting the sequence
   characters to lower-case, some non-EMBOSS programs e.g. fasta can
   interpret this as a masked region. The sequence is unchanged apart
   from the case change. You might like to ensure that the whole sequence
   is in upper-case before masking the specified regions to lower-case by
   using the '-supper' flag. Toggle value Yes/No No
   -maskchar Character to use when masking. Default is 'X' for protein
   sequences, 'N' for nucleic sequences. If the mask character is set to
   be the SPACE character or a null character, then the sequence is
   'masked' by changing it to lower-case, just as with the '-lowercase'
   flag. A string up to 1 characters 'X' for protein, 'N' for nucleic
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   maskfeat reads in a sequence USA. You can optionally specify a GFF
   feature file to use with the command-line option '-gff filename'.

  Input files for usage example

   'tembl:ab000360' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:ab000360

ID   AB000360   standard; DNA; HUM; 2582 BP.
XX
AC   AB000360;
XX
SV   AB000360.1
XX
DT   27-OCT-1997 (Rel. 53, Created)
DT   27-OCT-1997 (Rel. 53, Last updated, Version 1)
XX
DE   Homo sapiens PIGC gene, complete cds.
XX
KW   glycosylphosphatidylinositol-synthesis gene; PIGC.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-2582
RA   Hong Y.;
RT   ;
RL   Submitted (08-JAN-1997) to the EMBL/GenBank/DDBJ databases.
RL   Yeongjin Hong, Research Institute for Microbial Diseases, Immunoregulation
;
RL   3-1 Yamada-oka, Suita, Osaka 565, Japan
RL   (E-mail:kohishi@biken.osaka-u.ac.jp, Tel:81-6-879-8329, Fax:81-6-875-5233)
XX
RN   [2]
RA   Hong Y., Ohishi K., Inoue N., Endo Y., Fujita T., Takeda J., Kinoshita T.;
RT   "Structures and chromosomal localizations of the
RT   glycosylphosphatidylinositol synthesis gene PIGC and its pseudogene
RT   PIGCP1";
RL   Genomics 44:347-349(1997).
XX
DR   SWISS-PROT; Q92535; PIGC_HUMAN.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..2582
FT                   /chromosome="1"
FT                   /db_xref="taxon:9606"
FT                   /sequenced_mol="DNA"
FT                   /organism="Homo sapiens"
FT                   /map="1q23-q25"
FT   exon            808..2266
FT   CDS             1101..1994
FT                   /codon_start=1
FT                   /db_xref="SWISS-PROT:Q92535"
FT                   /transl_table=1
FT                   /gene="PIGC"
FT                   /standard_name="glycosylphosphatidylinositol-synthesis


  [Part of this file has been deleted for brevity]

FT   variation       2259
FT                   /replace="t"
FT   repeat_region   2331..2356
FT                   /rpt_unit=gt
XX
SQ   Sequence 2582 BP; 694 A; 494 C; 581 G; 813 T; 0 other;
     ggatccctgc tgcagagggg gtaacggtgt ctggcttgcc aagcaatatt tgttgtggtc        6
0
     tatcatggaa gaaataaagt cgggcaatat gaattttttt tttctcaaat ttgccggatg       12
0
     gctgtggtgt ttctgactct tagttttctc attgtgaaaa aggaatgatt atcttcttcg       18
0
     atcctctcaa gagtttcctt gttttgagta gattgatagc tctttaaagg atgctaagct       24
0
     cagctaatgg aagaagagtc tagtttcttt gaggctttga ttttggttaa actatagagc       30
0
     tcataccttt ctgtatggtg cagcttacta ttgtctttgg attggtaact taaaaaatac       36
0
     aaataacatg cctttgagaa ccaataaaaa ctatggatat tatccctata aatttacaca       42
0
     aatccagata taagcatgca atgtgatata cctaagggat atgtgaacca ctgagttaag       48
0
     aactgcttta gagggagata caatgtgaga cacaggcttt gggataagac tttggtttga       54
0
     atcctggctc tgctctgtta ccttagggca aagttactta agcatcttga atctcagctt       60
0
     ttttaccaaa gcaggactaa tactaactta caaggtggtg aggattaagt gaaagaagat       66
0
     acataaggca cttagcacat agtaggtact caataagcga tagctaacag atgtctatta       72
0
     ttattcaagg aattataatt ttcaaatctg aaatgcagtt ttaatgtccc ataaggtgac       78
0
     taccacatac atttttctca gacttttagt aaactgagtt gatttgactt tatctcagta       84
0
     ctactcttga cctttcacaa ctttcgtagg ttcacagtct ctctttttct aggaacttgg       90
0
     ctgtgttgtc ctgcctcaga gacaaattca tctattgtag gcctagcccc tgcctttgaa       96
0
     aacaaggaaa ggttggtaga acatcaacac agcatggaat ttccagggag gtctcatttc      102
0
     aaaacttcat aaagaacaag aaccacctgg acttctgtga gggcgatgat taaactggcc      108
0
     tgagtttgaa tgaaaggata atgtatgctc aacctgtgac taacaccaag gaggtcaagt      114
0
     ggcagaaggt cttgtatgag cgacagccct ttcctgataa ctatgtggac cggcgattcc      120
0
     tggaagagct ccggaaaaac atccatgctc ggaaatacca atattgggct gtggtatttg      126
0
     agtccagtgt ggtgatccag cagctgtgca gtgtttgtgt ttttgtggtt atctggtggt      132
0
     atatggatga gggtcttctg gccccccatt ggcttttagg gactggcctg gcttcttcac      138
0
     tgattgggta tgttttgttt gatctcattg atggaggtga agggcggaag aagagtgggc      144
0
     agacccggtg ggctgacctg aagagtgccc tagtcttcat tactttcact tatgggtttt      150
0
     caccagtgct gaagaccctt acagagtctg tcagcactga caccatctat gccatgtcag      156
0
     tcttcatgct gttaggccat ctcatctttt ttgactatgg tgccaatgct gccattgtat      162
0
     ccagcacact atccttgaac atggccatct ttgcttctgt atgcttggca tcacgtcttc      168
0
     cccggtccct gcatgccttc atcatggtga catttgccat tcagattttt gccctgtggc      174
0
     ccatgttgca gaagaaacta aaggcatgta ctccccggag ctatgtgggg gtcacactgc      180
0
     tttttgcatt ttcagccgtg ggaggcctac tgtccattag tgctgtggga gccgtactct      186
0
     ttgcccttct gctgatgtct atctcatgtc tgtgttcatt ctacctcatt cgcttgcagc      192
0
     tttttaaaga aaacattcat gggccttggg atgaagctga aatcaaggaa gacttgtcca      198
0
     ggttcctcag ttaaattagg acatccatta cattattaaa gcaagctgat agattagcct      204
0
     cctaactagt atagaactta aagacagagt tccattctgg aagcagcatg tcattgtggt      210
0
     aagagaatag agatcaaaac caaaaaaaat gaaccaaagg cttgggtggt gagggtgctt      216
0
     atcctttctg ttattttgta gatgaaaaaa ctttctgggg acctcttgaa ttacatgctg      222
0
     taacatatga agtgatgtgg tttctattaa aaaaataaca catccatcaa gttgtctcat      228
0
     gatttttcca taaacaggag gcagacagag gggcatgaag agtgaagtaa gtgtgtgtgt      234
0
     gtgtgtgtgt gtgtgtaaag tcacttcttt ctaccctttt caatgtgcta atgctctttt      240
0
     atttatctag ggctcaaatc ttagaacaca gggtgctatg ctcagttttg ttgcccaaga      246
0
     tcacagaatt ggttacttaa ccttgactca gagtttctac cttgttctta gggaagcata      252
0
     tcacaactaa ttgcaaagca gagtgtgatg tgtcacaata agcagaatgc tagggggaat      258
0
     tc                                                                     258
2
//

Output file format

   maskfeat writes out a normal, masked, sequence file.

  Output files for usage example

  File: ab000360.fasta

>AB000360 AB000360.1 Homo sapiens PIGC gene, complete cds.
ggatccctgctgcagagggggtaacggtgtctggcttgccaagcaatatttgttgtggtc
tatcatggaagaaataaagtcgggcaatatgaattttttttttctcaaatttgccggatg
gctgtggtgtttctgactcttagttttctcattgtgaaaaaggaatgattatcttcttcg
atcctctcaagagtttccttgttttgagtagattgatagctctttaaaggatgctaagct
cagctaatggaagaagagtctagtttctttgaggctttgattttggttaaactatagagc
tcatacctttctgtatggtgcagcttactattgtctttggattggtaacttaaaaaatac
aaataacatgcctttgagaaccaataaaaactatggatattatccctataaatttacaca
aatccagatataagcatgcaatgtgatatacctaagggatatgtgaaccactgagttaag
aactgctttagagggagatacaatgtgagacacaggctttgggataagactttggtttga
atcctggctctgctctgttaccttagggcaaagttacttaagcatcttgaatctcagctt
ttttaccaaagcaggactaatactaacttacaaggtggtgaggattaagtgaaagaagat
acataaggcacttagcacatagtaggtactcaataagcgatagctaacagatgtctatta
ttattcaaggaattataattttcaaatctgaaatgcagttttaatgtcccataaggtgac
taccacatacatttttctcagacttttagtaaactgagttgatttgactttatctcagta
ctactcttgacctttcacaactttcgtaggttcacagtctctctttttctaggaacttgg
ctgtgttgtcctgcctcagagacaaattcatctattgtaggcctagcccctgcctttgaa
aacaaggaaaggttggtagaacatcaacacagcatggaatttccagggaggtctcatttc
aaaacttcataaagaacaagaaccacctggacttctgtgagggcgatgattaaactggcc
tgagtttgaatgaaaggataatgtatgctcaacctgtgactaacaccaaggaggtcaagt
ggcagaaggtcttgtatgagcgacagccctttcctgataactatgtggaccggcgattcc
tggaagagctccggaaaaacatccatgctcggaaataccaatattgggctgtggtatttg
agtccagtgtggtgatccagcagctgtgcagtgtttgtgtttttgtggttatctggtggt
atatggatgagggtcttctggccccccattggcttttagggactggcctggcttcttcac
tgattgggtatgttttgtttgatctcattgatggaggtgaagggcggaagaagagtgggc
agacccggtgggctgacctgaagagtgccctagtcttcattactttcacttatgggtttt
caccagtgctgaagacccttacagagtctgtcagcactgacaccatctatgccatgtcag
tcttcatgctgttaggccatctcatcttttttgactatggtgccaatgctgccattgtat
ccagcacactatccttgaacatggccatctttgcttctgtatgcttggcatcacgtcttc
cccggtccctgcatgccttcatcatggtgacatttgccattcagatttttgccctgtggc
ccatgttgcagaagaaactaaaggcatgtactccccggagctatgtgggggtcacactgc
tttttgcattttcagccgtgggaggcctactgtccattagtgctgtgggagccgtactct
ttgcccttctgctgatgtctatctcatgtctgtgttcattctacctcattcgcttgcagc
tttttaaagaaaacattcatgggccttgggatgaagctgaaatcaaggaagacttgtcca
ggttcctcagttaaattaggacatccattacattattaaagcaagctgatagattagcct
cctaactagtatagaacttaaagacagagttccattctggaagcagcatgtcattgtggt
aagagaatagagatcaaaaccaaaaaaaatgaaccaaaggcttgggtggtgagggtgctt
atcctttctgttattttgtagatgaaaaaactttctggggacctcttgaattacatgctg
taacatatgaagtgatgtggtttctattaaaaaaataacacatccatcaagttgtctcat
gatttttccataaacaggaggcagacagaggggcatgaagagtgaagtaaNNNNNNNNNN
NNNNNNNNNNNNNNNNaaagtcacttctttctacccttttcaatgtgctaatgctctttt
atttatctagggctcaaatcttagaacacagggtgctatgctcagttttgttgcccaaga
tcacagaattggttacttaaccttgactcagagtttctaccttgttcttagggaagcata
tcacaactaattgcaaagcagagtgtgatgtgtcacaataagcagaatgctagggggaat
tc

  Output files for usage example 2

  File: ab000360.fasta

>AB000360 AB000360.1 Homo sapiens PIGC gene, complete cds.
GGATCCCTGCTGCAGAGGGGGTAACGGTGTCTGGCTTGCCAAGCAATATTTGTTGTGGTC
TATCATGGAAGAAATAAAGTCGGGCAATATGAATTTTTTTTTTCTCAAATTTGCCGGATG
GCTGTGGTGTTTCTGACTCTTAGTTTTCTCATTGTGAAAAAGGAATGATTATCTTCTTCG
ATCCTCTCAAGAGTTTCCTTGTTTTGAGTAGATTGATAGCTCTTTAAAGGATGCTAAGCT
CAGCTAATGGAAGAAGAGTCTAGTTTCTTTGAGGCTTTGATTTTGGTTAAACTATAGAGC
TCATACCTTTCTGTATGGTGCAGCTTACTATTGTCTTTGGATTGGTAACTTAAAAAATAC
AAATAACATGCCTTTGAGAACCAATAAAAACTATGGATATTATCCCTATAAATTTACACA
AATCCAGATATAAGCATGCAATGTGATATACCTAAGGGATATGTGAACCACTGAGTTAAG
AACTGCTTTAGAGGGAGATACAATGTGAGACACAGGCTTTGGGATAAGACTTTGGTTTGA
ATCCTGGCTCTGCTCTGTTACCTTAGGGCAAAGTTACTTAAGCATCTTGAATCTCAGCTT
TTTTACCAAAGCAGGACTAATACTAACTTACAAGGTGGTGAGGATTAAGTGAAAGAAGAT
ACATAAGGCACTTAGCACATAGTAGGTACTCAATAAGCGATAGCTAACAGATGTCTATTA
TTATTCAAGGAATTATAATTTTCAAATCTGAAATGCAGTTTTAATGTCCCATAAGGTGAC
TACCACATACATTTTTCTCAGACTTTTAGTAAACTGAGTTGATTTGACTTTATCTCAGTA
CTACTCTTGACCTTTCACAACTTTCGTAGGTTCACAGTCTCTCTTTTTCTAGGAACTTGG
CTGTGTTGTCCTGCCTCAGAGACAAATTCATCTATTGTAGGCCTAGCCCCTGCCTTTGAA
AACAAGGAAAGGTTGGTAGAACATCAACACAGCATGGAATTTCCAGGGAGGTCTCATTTC
AAAACTTCATAAAGAACAAGAACCACCTGGACTTCTGTGAGGGCGATGATTAAACTGGCC
TGAGTTTGAATGAAAGGATAATGTATGCTCAACCTGTGACTAACACCAAGGAGGTCAAGT
GGCAGAAGGTCTTGTATGAGCGACAGCCCTTTCCTGATAACTATGTGGACCGGCGATTCC
TGGAAGAGCTCCGGAAAAACATCCATGCTCGGAAATACCAATATTGGGCTGTGGTATTTG
AGTCCAGTGTGGTGATCCAGCAGCTGTGCAGTGTTTGTGTTTTTGTGGTTATCTGGTGGT
ATATGGATGAGGGTCTTCTGGCCCCCCATTGGCTTTTAGGGACTGGCCTGGCTTCTTCAC
TGATTGGGTATGTTTTGTTTGATCTCATTGATGGAGGTGAAGGGCGGAAGAAGAGTGGGC
AGACCCGGTGGGCTGACCTGAAGAGTGCCCTAGTCTTCATTACTTTCACTTATGGGTTTT
CACCAGTGCTGAAGACCCTTACAGAGTCTGTCAGCACTGACACCATCTATGCCATGTCAG
TCTTCATGCTGTTAGGCCATCTCATCTTTTTTGACTATGGTGCCAATGCTGCCATTGTAT
CCAGCACACTATCCTTGAACATGGCCATCTTTGCTTCTGTATGCTTGGCATCACGTCTTC
CCCGGTCCCTGCATGCCTTCATCATGGTGACATTTGCCATTCAGATTTTTGCCCTGTGGC
CCATGTTGCAGAAGAAACTAAAGGCATGTACTCCCCGGAGCTATGTGGGGGTCACACTGC
TTTTTGCATTTTCAGCCGTGGGAGGCCTACTGTCCATTAGTGCTGTGGGAGCCGTACTCT
TTGCCCTTCTGCTGATGTCTATCTCATGTCTGTGTTCATTCTACCTCATTCGCTTGCAGC
TTTTTAAAGAAAACATTCATGGGCCTTGGGATGAAGCTGAAATCAAGGAAGACTTGTCCA
GGTTCCTCAGTTAAATTAGGACATCCATTACATTATTAAAGCAAGCTGATAGATTAGCCT
CCTAACTAGTATAGAACTTAAAGACAGAGTTCCATTCTGGAAGCAGCATGTCATTGTGGT
AAGAGAATAGAGATCAAAACCAAAAAAAATGAACCAAAGGCTTGGGTGGTGAGGGTGCTT
ATCCTTTCTGTTATTTTGTAGATGAAAAAACTTTCTGGGGACCTCTTGAATTACATGCTG
TAACATATGAAGTGATGTGGTTTCTATTAAAAAAATAACACATCCATCAAGTTGTCTCAT
GATTTTTCCATAAACAGGAGGCAGACAGAGGGGCATGAAGAGTGAAGTAAgtgtgtgtgt
gtgtgtgtgtgtgtgtAAAGTCACTTCTTTCTACCCTTTTCAATGTGCTAATGCTCTTTT
ATTTATCTAGGGCTCAAATCTTAGAACACAGGGTGCTATGCTCAGTTTTGTTGCCCAAGA
TCACAGAATTGGTTACTTAACCTTGACTCAGAGTTTCTACCTTGTTCTTAGGGAAGCATA
TCACAACTAATTGCAAAGCAGAGTGTGATGTGTCACAATAAGCAGAATGCTAGGGGGAAT
TC

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name                          Description
   biosed       Replace or delete sequence sections
   coderet      Extract CDS, mRNA and translations from feature tables
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Writes a list file of the logical OR of two sets of sequences
   maskseq      Mask off regions of a sequence
   newseq       Type in a short new sequence
   noreturn     Removes carriage return from ASCII files
   notseq       Excludes a set of sequences and writes out the remaining ones
   nthseq       Writes one sequence from a multiple set of sequences
   pasteseq     Insert one sequence into another
   revseq       Reverse and complement a sequence
   seqret       Reads and writes (returns) sequences
   seqretsplit  Reads and writes (returns) sequences in individual files
   showfeat     Show features of a sequence
   skipseq      Reads and writes (returns) sequences, skipping the first few
   splitter     Split a sequence into (overlapping) smaller sequences
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   twofeat      Finds neighbouring pairs of features in sequences
   union        Reads sequence fragments and builds one sequence
   vectorstrip  Strips out DNA between a pair of vector sequences
   yank         Reads a sequence range, appends the full USA to a list file

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 (2000) - Gary Williams

Target users

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

Comments

   None
