maskfeat |
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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.
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
Write a sequence with masked features Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Sequence(s) filename and optional format, or reference (input USA) [-outseq] seqout [ |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-sequence] (Parameter 1) |
seqall | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
[-outseq] (Parameter 2) |
seqout | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format |
Additional (Optional) qualifiers | ||||
-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://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html 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 | 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. | Toggle value Yes/No | No |
-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. | Any string up to 1 characters | 'X' for protein, 'N' for nucleic |
Advanced (Unprompted) qualifiers | ||||
(none) | ||||
Associated qualifiers | ||||
"-sequence" associated seqall qualifiers | ||||
-sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
-send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
-sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
-sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
-snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
-sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
-slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
-supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
-sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
-sdbname1 -sdbname_sequence |
string | Database name | Any string | |
-sid1 -sid_sequence |
string | Entryname | Any string | |
-ufo1 -ufo_sequence |
string | UFO features | Any string | |
-fformat1 -fformat_sequence |
string | Features format | Any string | |
-fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
"-outseq" associated seqout qualifiers | ||||
-osformat2 -osformat_outseq |
string | Output seq format | Any string | |
-osextension2 -osextension_outseq |
string | File name extension | Any string | |
-osname2 -osname_outseq |
string | Base file name | Any string | |
-osdirectory2 -osdirectory_outseq |
string | Output directory | Any string | |
-osdbname2 -osdbname_outseq |
string | Database name to add | Any string | |
-ossingle2 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N |
-oufo2 -oufo_outseq |
string | UFO features | Any string | |
-offormat2 -offormat_outseq |
string | Features format | Any string | |
-ofname2 -ofname_outseq |
string | Features file name | Any string | |
-ofdirectory2 -ofdirectory_outseq |
string | Output directory | Any string | |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
The input is a standard EMBOSS sequence query (also known as a 'USA') with associated feature information.
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: text, html, xml (uniprotxml), obo, embl (swissprot)
Where the sequence format has no feature information, a second file can be read to load the feature data. The file is specified with the qualifier -ufo xxx and the feature format is specified with the qualifier -fformat xxx
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
See: http://emboss.sf.net/docs/themes/FeatureFormats.html for further information on feature formats.
ID AB000360; SV 1; linear; genomic DNA; STD; HUM; 2582 BP. XX AC AB000360; XX DT 27-OCT-1997 (Rel. 53, Created) DT 28-SEP-2008 (Rel. 97, Last updated, Version 5) XX DE Homo sapiens PIGC gene, complete cds. XX KW . 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., Ohishi K., Inoue N., Endo Y., Fujita T., Takeda J., Kinoshita T.; RT ; RL Submitted (08-JAN-1997) to the EMBL/GenBank/DDBJ databases. RL Contact:Yeongjin Hong Research Institute for Microbial Diseases, RL Immunoregulation; 3-1 Yamada-oka, Suita, Osaka 565, Japan 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" FT /db_xref="GOA:Q92535" [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 // |
The output is a standard EMBOSS sequence file.
The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
The sequence file has features masked with the specified character.
>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 |
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://www.ebi.ac.uk/Services/WebFeat/ (EMBL feature types) and see Appendix A of the Swissprot user manual in http://www.uniprot.org/manual/sequence_annotation (Swissprot feature types).
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 |
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 |
feattext | Return a feature table original text |
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 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 |
nthseqset | Reads and writes (returns) one set of sequences from many |
pasteseq | Insert one sequence into another |
revseq | Reverse and complement a nucleotide sequence |
seqcount | Reads and counts sequences |
seqret | Reads and writes (returns) sequences |
seqretsetall | Reads and writes (returns) many sets of 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 |
splitsource | Split sequence(s) into original source sequences |
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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.