|   | maskfeat | 
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.
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
| 
   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
  [-outseq]            seqout     [ | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| [-outseq] (Parameter 2) | Sequence filename and optional format (output USA) | Writeable 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. | Any string up to 1 characters | 'X' for protein, 'N' for nucleic | 
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
| 
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        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
//
 | 
| >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 | 
| >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 | 
| Program name | Description | 
|---|---|
| biosed | Replace or delete sequence sections | 
| codcopy | Reads and writes a codon usage table | 
| 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 | 
| extractalign | Extract regions from a sequence alignment | 
| extractfeat | Extract features from a sequence | 
| extractseq | Extract regions from a sequence | 
| listor | Write a list file of the logical OR of two sets of sequences | 
| makenucseq | Creates random nucleotide sequences | 
| makeprotseq | Creates random protein sequences | 
| maskseq | Mask off regions of a sequence | 
| newseq | Type in a short new sequence | 
| noreturn | Removes carriage return from ASCII files | 
| notseq | Exclude a set of sequences and write 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 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 |