| 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

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

       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            boolean    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 qualifiers: (none)
       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outseq" related 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

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
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. | Boolean 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. | Any string is accepted | 'X' for protein, 'N' for nucleic
Advanced 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        60
         tatcatggaa gaaataaagt cgggcaatat gaattttttt tttctcaaat ttgccggatg       120
         gctgtggtgt ttctgactct tagttttctc attgtgaaaa aggaatgatt atcttcttcg       180
         atcctctcaa gagtttcctt gttttgagta gattgatagc tctttaaagg atgctaagct       240
         cagctaatgg aagaagagtc tagtttcttt gaggctttga ttttggttaa actatagagc       300
         tcataccttt ctgtatggtg cagcttacta ttgtctttgg attggtaact taaaaaatac       360
         aaataacatg cctttgagaa ccaataaaaa ctatggatat tatccctata aatttacaca       420
         aatccagata taagcatgca atgtgatata cctaagggat atgtgaacca ctgagttaag       480
         aactgcttta gagggagata caatgtgaga cacaggcttt gggataagac tttggtttga       540
         atcctggctc tgctctgtta ccttagggca aagttactta agcatcttga atctcagctt       600
         ttttaccaaa gcaggactaa tactaactta caaggtggtg aggattaagt gaaagaagat       660
         acataaggca cttagcacat agtaggtact caataagcga tagctaacag atgtctatta       720
         ttattcaagg aattataatt ttcaaatctg aaatgcagtt ttaatgtccc ataaggtgac       780
         taccacatac atttttctca gacttttagt aaactgagtt gatttgactt tatctcagta       840
         ctactcttga cctttcacaa ctttcgtagg ttcacagtct ctctttttct aggaacttgg       900
         ctgtgttgtc ctgcctcaga gacaaattca tctattgtag gcctagcccc tgcctttgaa       960
         aacaaggaaa ggttggtaga acatcaacac agcatggaat ttccagggag gtctcatttc      1020
         aaaacttcat aaagaacaag aaccacctgg acttctgtga gggcgatgat taaactggcc      1080
         tgagtttgaa tgaaaggata atgtatgctc aacctgtgac taacaccaag gaggtcaagt      1140
         ggcagaaggt cttgtatgag cgacagccct ttcctgataa ctatgtggac cggcgattcc      1200
         tggaagagct ccggaaaaac atccatgctc ggaaatacca atattgggct gtggtatttg      1260
         agtccagtgt ggtgatccag cagctgtgca gtgtttgtgt ttttgtggtt atctggtggt      1320
         atatggatga gggtcttctg gccccccatt ggcttttagg gactggcctg gcttcttcac      1380
         tgattgggta tgttttgttt gatctcattg atggaggtga agggcggaag aagagtgggc      1440
         agacccggtg ggctgacctg aagagtgccc tagtcttcat tactttcact tatgggtttt      1500
         caccagtgct gaagaccctt acagagtctg tcagcactga caccatctat gccatgtcag      1560
         tcttcatgct gttaggccat ctcatctttt ttgactatgg tgccaatgct gccattgtat      1620
         ccagcacact atccttgaac atggccatct ttgcttctgt atgcttggca tcacgtcttc      1680
         cccggtccct gcatgccttc atcatggtga catttgccat tcagattttt gccctgtggc      1740
         ccatgttgca gaagaaacta aaggcatgta ctccccggag ctatgtgggg gtcacactgc      1800
         tttttgcatt ttcagccgtg ggaggcctac tgtccattag tgctgtggga gccgtactct      1860
         ttgcccttct gctgatgtct atctcatgtc tgtgttcatt ctacctcatt cgcttgcagc      1920
         tttttaaaga aaacattcat gggccttggg atgaagctga aatcaaggaa gacttgtcca      1980
         ggttcctcag ttaaattagg acatccatta cattattaaa gcaagctgat agattagcct      2040
         cctaactagt atagaactta aagacagagt tccattctgg aagcagcatg tcattgtggt      2100
         aagagaatag agatcaaaac caaaaaaaat gaaccaaagg cttgggtggt gagggtgctt      2160
         atcctttctg ttattttgta gatgaaaaaa ctttctgggg acctcttgaa ttacatgctg      2220
         taacatatga agtgatgtgg tttctattaa aaaaataaca catccatcaa gttgtctcat      2280
         gatttttcca taaacaggag gcagacagag gggcatgaag agtgaagtaa gtgtgtgtgt      2340
         gtgtgtgtgt gtgtgtaaag tcacttcttt ctaccctttt caatgtgcta atgctctttt      2400
         atttatctag ggctcaaatc ttagaacaca gggtgctatg ctcagttttg ttgcccaaga      2460
         tcacagaatt ggttacttaa ccttgactca gagtttctac cttgttctta gggaagcata      2520
         tcacaactaa ttgcaaagca gagtgtgatg tgtcacaata agcagaatgc tagggggaat      2580
         tc                                                                     2582
    //

## 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

maskseq simply masks a user-specified set of regions, without using annotated features.

## Author(s)

Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, 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