
                                 maskfeat 



Function

   Write a sequence with masked features

Description

   maskfeat reads a sequence with associated features and writes the same
   information to file but with features of the specified type omitted
   (masked). Sequence regions corresponding to the masked-out features
   are masked such that characters in those region are (optionally)
   converted to lower case and / or (optionally) replaced with the
   specified mask 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 
Write a sequence with masked features
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 
Write a sequence with masked features
output sequence [ab000360.fasta]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
  [-outseq]            seqout     [.] Sequence filename and
                                  optional format (output USA)

   Additional (Optional) qualifiers (* if not always prompted):
   -type               string     [repeat*] 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)
   -tolower            toggle     [N] 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     ['X' for protein, 'N' for nucleic] 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. (Any string up to 1 characters)

   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 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. 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

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; SV 1; linear; genomic DNA; STD; HUM; 2582 BP.
XX
AC   AB000360;
XX
DT   27-OCT-1997 (Rel. 53, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 3)
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; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   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]
RX   DOI; 10.1006/geno.1997.4893.
RX   PUBMED; 9325057.
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(3):347-349(1997).
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..2582
FT                   /organism="Homo sapiens"
FT                   /chromosome="1"
FT                   /map="1q23-q25"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:9606"
FT   exon            808..2266
FT   CDS             1101..1994
FT                   /codon_start=1
FT                   /transl_table=1
FT                   /gene="PIGC"
FT                   /standard_name="glycosylphosphatidylinositol-synthesis
FT                   gene"
FT                   /db_xref="GDB:6045444"


  [Part of this file has been deleted for brevity]

FT   variation       2259
FT                   /replace="t"
FT   repeat_region   2331..2356
FT                   /rpt_unit_seq="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

   Formats such as EMBL or SWISSPROT include features in the sequence
   annotation. Otherwise, features they may be supplied in a separate
   file and specified with the qualifier -ufo or -fopenfile / -fformat.

   The feature type to mask is by default repeat*, i.e. any type whose
   name starts with repeat will be omitted from the output file. Any
   other type of feature(s) may be specified with the -type qualifier. To
   specify more than one type of feature, separate their names with
   spaces or commas. The names 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/ (EMBL feature types) and see
   Appendix A of the Swissprot user manual in
   http://www.expasy.ch/txt/userman.txt (Swissprot feature types).

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
   aligncopy Reads and writes alignments
   aligncopypair Reads and writes pairs from alignments
   biosed Replace or delete sequence sections
   codcopy Copy and reformat a codon usage table
   coderet Extract CDS, mRNA and translations from feature tables
   cutseq Removes a section from a sequence
   degapseq Removes non-alphabetic (e.g. gap) characters from sequences
   descseq Alter the name or description of a sequence
   entret Retrieves sequence entries from flatfile databases and files
   extractalign Extract regions from a sequence alignment
   extractfeat Extract features from sequence(s)
   extractseq Extract regions from a sequence
   featcopy Reads and writes a feature table
   featreport Reads and writes a feature table
   listor Write a list file of the logical OR of two sets of sequences
   makenucseq Create random nucleotide sequences
   makeprotseq Create random protein sequences
   maskambignuc Masks all ambiguity characters in nucleotide sequences
   with N
   maskambigprot Masks all ambiguity characters in protein sequences with
   X
   maskseq Write a sequence with masked regions
   newseq Create a sequence file from a typed-in sequence
   nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file
   noreturn Remove carriage return from ASCII files
   nospace Remove all whitespace from an ASCII text file
   notab Replace tabs with spaces in an ASCII text file
   notseq Write to file a subset of an input stream of sequences
   nthseq Write to file a single sequence from an input stream of
   sequences
   pasteseq Insert one sequence into another
   revseq Reverse and complement a nucleotide sequence
   seqret Reads and writes (returns) sequences
   seqretsplit Reads sequences and writes them to individual files
   showfeat Display features of a sequence in pretty format
   sizeseq Sort sequences by size
   skipredundant Remove redundant sequences from an input set
   skipseq Reads and writes (returns) sequences, skipping first few
   splitter Split sequence(s) into smaller sequences
   trimest Remove poly-A tails from nucleotide sequences
   trimseq Remove unwanted characters from start and end of sequence(s)
   trimspace Remove extra whitespace from an ASCII text file
   twofeat Finds neighbouring pairs of features in sequence(s)
   union Concatenate multiple sequences into a single sequence
   vectorstrip Removes vectors from the ends of nucleotide sequence(s)
   yank Add a sequence reference (a 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
