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 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) |
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 // |
>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 |
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 |
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 |