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|
<HTML>
<HEAD>
<TITLE>
EMBOSS: maskfeat
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
maskfeat
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Mask off features of a sequence
<H2>
Description
</H2>
<b>maskfeat</b> 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'.
<p>
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.
<p>
If you are unsure of the names of feature types in use, please consult
<A HREF="http://www3.ebi.ac.uk/Services/WebFeat/">
http://www3.ebi.ac.uk/Services/WebFeat/</A>
for a list of the EMBL feature types and see Appendix A of the Swissprot
user manual in
<A HREF="http://www.expasy.ch/txt/userman.txt">
http://www.expasy.ch/txt/userman.txt</A>
for a list of the Swissprot feature types.
<p>
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.
<p>
Some non-EMBOSS programs (for example FASTA) are capable of treating
lower-case regions as if they are masked. <b>maskfeat</b> 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.
<H2>
Usage
</H2>
<b>Here is a sample session with maskfeat</b>
<p>
Mask out a feature whose type is "repeat_region" from position 2331 to 2356:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>maskfeat tembl:ab000360 </b>
Mask off features of a sequence.
output sequence [ab000360.fasta]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<p>
<b>Example 2</b>
<p>
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:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>maskfeat tembl:ab000360 -tolower -supper </b>
Mask off features of a sequence.
output sequence [ab000360.fasta]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#output.2">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-sequence] seqall Sequence(s) filename and optional format, or
reference (input USA)
[-outseq] seqout [<sequence>.<format>] 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://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)
-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
-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 dying program messages
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outseq]<br>(Parameter 2)</td>
<td>Sequence filename and optional format (output USA)</td>
<td>Writeable sequence</td>
<td><i><*></i>.<i>format</i></td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-type</td>
<td>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*</td>
<td>Any string is accepted</td>
<td>repeat*</td>
</tr>
<tr>
<td>-tolower</td>
<td>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.</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-maskchar</td>
<td>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.</td>
<td>Any string up to 1 characters</td>
<td>'X' for protein, 'N' for nucleic</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>maskfeat</b> reads in a sequence USA. You can optionally specify a
GFF feature file to use with the command-line option '-gff filename'.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:ab000360' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:ab000360</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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"
<font color=red> [Part of this file has been deleted for brevity]</font>
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
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<b>maskfeat</b> writes out a normal, masked, sequence file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: ab000360.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>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
</pre>
</td></tr></table><p>
<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: ab000360.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>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
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with a status of 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="biosed.html">biosed</a></td>
<td>Replace or delete sequence sections</td>
</tr>
<tr>
<td><a href="codcopy.html">codcopy</a></td>
<td>Reads and writes a codon usage table</td>
</tr>
<tr>
<td><a href="coderet.html">coderet</a></td>
<td>Extract CDS, mRNA and translations from feature tables</td>
</tr>
<tr>
<td><a href="cutseq.html">cutseq</a></td>
<td>Removes a specified section from a sequence</td>
</tr>
<tr>
<td><a href="degapseq.html">degapseq</a></td>
<td>Removes gap characters from sequences</td>
</tr>
<tr>
<td><a href="descseq.html">descseq</a></td>
<td>Alter the name or description of a sequence</td>
</tr>
<tr>
<td><a href="entret.html">entret</a></td>
<td>Reads and writes (returns) flatfile entries</td>
</tr>
<tr>
<td><a href="extractalign.html">extractalign</a></td>
<td>Extract regions from a sequence alignment</td>
</tr>
<tr>
<td><a href="extractfeat.html">extractfeat</a></td>
<td>Extract features from a sequence</td>
</tr>
<tr>
<td><a href="extractseq.html">extractseq</a></td>
<td>Extract regions from a sequence</td>
</tr>
<tr>
<td><a href="listor.html">listor</a></td>
<td>Write a list file of the logical OR of two sets of sequences</td>
</tr>
<tr>
<td><a href="makenucseq.html">makenucseq</a></td>
<td>Creates random nucleotide sequences</td>
</tr>
<tr>
<td><a href="makeprotseq.html">makeprotseq</a></td>
<td>Creates random protein sequences</td>
</tr>
<tr>
<td><a href="maskseq.html">maskseq</a></td>
<td>Mask off regions of a sequence</td>
</tr>
<tr>
<td><a href="newseq.html">newseq</a></td>
<td>Type in a short new sequence</td>
</tr>
<tr>
<td><a href="noreturn.html">noreturn</a></td>
<td>Removes carriage return from ASCII files</td>
</tr>
<tr>
<td><a href="notseq.html">notseq</a></td>
<td>Exclude a set of sequences and write out the remaining ones</td>
</tr>
<tr>
<td><a href="nthseq.html">nthseq</a></td>
<td>Writes one sequence from a multiple set of sequences</td>
</tr>
<tr>
<td><a href="pasteseq.html">pasteseq</a></td>
<td>Insert one sequence into another</td>
</tr>
<tr>
<td><a href="revseq.html">revseq</a></td>
<td>Reverse and complement a sequence</td>
</tr>
<tr>
<td><a href="seqret.html">seqret</a></td>
<td>Reads and writes (returns) sequences</td>
</tr>
<tr>
<td><a href="seqretsplit.html">seqretsplit</a></td>
<td>Reads and writes (returns) sequences in individual files</td>
</tr>
<tr>
<td><a href="showfeat.html">showfeat</a></td>
<td>Show features of a sequence</td>
</tr>
<tr>
<td><a href="skipseq.html">skipseq</a></td>
<td>Reads and writes (returns) sequences, skipping first few</td>
</tr>
<tr>
<td><a href="splitter.html">splitter</a></td>
<td>Split a sequence into (overlapping) smaller sequences</td>
</tr>
<tr>
<td><a href="trimest.html">trimest</a></td>
<td>Trim poly-A tails off EST sequences</td>
</tr>
<tr>
<td><a href="trimseq.html">trimseq</a></td>
<td>Trim ambiguous bits off the ends of sequences</td>
</tr>
<tr>
<td><a href="twofeat.html">twofeat</a></td>
<td>Finds neighbouring pairs of features in sequences</td>
</tr>
<tr>
<td><a href="union.html">union</a></td>
<td>Reads sequence fragments and builds one sequence</td>
</tr>
<tr>
<td><a href="vectorstrip.html">vectorstrip</a></td>
<td>Strips out DNA between a pair of vector sequences</td>
</tr>
<tr>
<td><a href="yank.html">yank</a></td>
<td>Reads a sequence range, appends the full USA to a list file</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
<H2>
History
</H2>
Written (2000) - Gary Williams
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
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