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|
maskfeat
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
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
Write a sequence with masked features
Version: EMBOSS:6.6.0.0
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://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)
-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
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-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 and exit. 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
-version boolean Report version number and exit
Input file format
maskfeat reads one or more nucleotide or protein sequences with
features.
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.
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 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 INSDC.
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
DR Ensembl-Gn; ENSG00000135845; Homo_sapiens.
DR Ensembl-Tr; ENST00000258324; Homo_sapiens.
DR Ensembl-Tr; ENST00000344529; Homo_sapiens.
DR Ensembl-Tr; ENST00000367728; Homo_sapiens.
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
[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
//
Output file format
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.
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://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).
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 Read and write alignments
aligncopypair Read and write pairs from alignments
biosed Replace or delete sequence sections
codcopy Copy and reformat a codon usage table
cutseq Remove a section from a sequence
degapseq Remove non-alphabetic (e.g. gap) characters from sequences
descseq Alter the name or description of a sequence
entret Retrieve 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 Read and write a feature table
featmerge Merge two overlapping feature tables
featreport Read and write 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 Mask all ambiguity characters in nucleotide sequences with
N
maskambigprot Mask 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 Read and write (return) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqcount Read and count sequences
seqret Read and write (return) sequences
seqretsetall Read and write (return) many sets of sequences
seqretsplit Read sequences and write 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 Read and write (return) 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 Find neighbouring pairs of features in sequence(s)
union Concatenate multiple sequences into a single sequence
vectorstrip Remove vectors from the ends of nucleotide sequence(s)
yank Add a sequence reference (a full USA) to a list file
Author(s)
Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
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
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