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<HTML>
<HEAD>
<TITLE>
EMBOSS: coderet
</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">
coderet
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Extract CDS, mRNA and translations from feature tables
<H2>
Description
</H2>
The feature table of sequence database entries often have sections like this:
<p>
This specifies that the coding sequence for the gene is constructed by
joining several sections of code, many of which are in other entries in
this database.
<p>
<hr>
<pre>
FT CDS join(U21925.1:818..987,U21926.1:258..420,
FT U21927.1:428..520,U21928.1:196..336,U21929.1:279..415,
FT U21930.1:895..1014,516..708)
</pre>
<hr>
<p>
or:
<p>
This specifies that the messenger RNA sequence for the gene is constructed by
joining several sections of code, many of which are in other entries in
this database.
<p>
<hr>
<pre>
FT mRNA join(M88628.1:1006..1318,M88629.1:221..342,
FT M88630.1:101..223,M88631.1:46..258,M88632.1:104..172,
FT M88633.1:387..503,M88634.1:51..272,M88635.1:303..564,
FT M88635.1:849..1020,M88636.1:282..375,M88637.1:39..253,
FT M88638.1:91..241,M88639.1:168..377,M88640.1:627..3732,
FT M88641.1:158..311,M88642.1:1051..1263,M88642.1:1550..1778,
FT M88642.1:1986..2168,M88642.1:3904..4020,
FT M88642.1:4627..4698,M88643.1:39..124,M88644.1:42..197,
FT M88645.1:542..686,M88646.1:75..223,M88647.1:109..285,
FT 253..2211)
</pre>
<hr>
<p>
or:
<p>
This specifies that the translation of the coding region is as follows.
<p>
<hr>
<pre>
FT /translation="MAQDSVDLSCDYQFWMQKLSVWDQASTLETQQDTCLHVAQFQEFL
FT RKMYEALKEMDSNTVIERFPTIGQLLAKACWNPFILAYDESQKILIWCLCCLINKEPQN
FT SGQSKLNSWIQGVLSHILSALRFDKEVALFTQGLGYAPIDYYPGLLKNMVLSLASELRE
FT NHLNGFNTQRRMAPERVASLSRVCVPLITLTDVDPLVEALLICHGREPQEILQPEFFEA
FT VNEAILLKKISLPMSAVVCLWLRHLPSLEKAMLHLFEKLISSERNCLRRIECFIKDSSL
FT PQAACHPAIFRVDEMFRCALLETDGALEIIATIQVFTQCFVEALEKASKQLRFALKTYF
FT PYTSPSLAMVLLQDPQDIPRGHWLQTLKHISELLREAVEDQTHGSCGGPFESWFLFIHF
FT GGWAEMVAEQLLMSAAEPPTALLWLLAFYYGPRDGRQQRAQTMVQVKAVLGHLLAMSRS
FT SSLSAQDLQTVAGQGTDTDLRAPAQQLIRHLLLNFLLWAPGGHTIAWDVITLMAHTAEI
FT THEIIGFLDQTLYRWNRLGIESPRSEKLARELLKELRTQV"
</pre>
<hr>
<p>
It is often a tedious and error-prone job to extract the several
sections of these sequences from the database entries and to join them together
to construct the indicated finished sequence.
<p>
<b>coderet</b> does this job for you.
<p>
You specify the sequence containing the feature table and it extracts
the required CDS, mRNA and/or protein sequences specified by this
feature table. If any sequences are in other entries of that database,
they are automatically fetched and incorporated correctly into the final
sequence.
<p>
The translations are not made from the coding sequence, they are extracted
directly from the translation sequence held in the feature table.
<H2>
Usage
</H2>
<b>Here is a sample session with coderet</b>
<p>
To extract all of the CDS, mRNA, non-coding and the protein translations:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>coderet </b>
Extract CDS, mRNA and translations from feature tables
Input nucleotide sequence(s): <b>tembl:x03487</b>
Output file [x03487.coderet]: <b></b>
Coding nucleotide output sequence(s) (optional) [x03487.cds]: <b></b>
Messenger RNA nucleotide output sequence(s) (optional) [x03487.mrna]: <b></b>
Translated coding protein output sequence(s) (optional) [x03487.prot]: <b></b>
Non-coding nucleotide output sequence(s) (optional) [x03487.noncoding]: <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>
To only extract the mRNA sequence:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>coderet -nocds -notranslation -norest </b>
Extract CDS, mRNA and translations from feature tables
Input nucleotide sequence(s): <b>tembl:X03487</b>
Output file [x03487.coderet]: <b></b>
Messenger RNA nucleotide output sequence(s) (optional) [x03487.mrna]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.2">Go to the input files for this example</a><br><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:
[-seqall] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
[-outfile] outfile [*.coderet] Output file name
[-cdsoutseq] seqoutall [<sequence>.<format>] Coding nucleotide
output sequence(s) (optional)
[-mrnaoutseq] seqoutall [<sequence>.<format>] Messenger RNA
nucleotide output sequence(s) (optional)
[-translationoutseq] seqoutall [<sequence>.<format>] Translated coding
protein output sequence(s) (optional)
[-restoutseq] seqoutall [<sequence>.<format>] Non-coding nucleotide
output sequence(s) (optional)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-seqall" 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
"-outfile" associated qualifiers
-odirectory2 string Output directory
"-cdsoutseq" associated qualifiers
-osformat3 string Output seq format
-osextension3 string File name extension
-osname3 string Base file name
-osdirectory3 string Output directory
-osdbname3 string Database name to add
-ossingle3 boolean Separate file for each entry
-oufo3 string UFO features
-offormat3 string Features format
-ofname3 string Features file name
-ofdirectory3 string Output directory
"-mrnaoutseq" associated qualifiers
-osformat4 string Output seq format
-osextension4 string File name extension
-osname4 string Base file name
-osdirectory4 string Output directory
-osdbname4 string Database name to add
-ossingle4 boolean Separate file for each entry
-oufo4 string UFO features
-offormat4 string Features format
-ofname4 string Features file name
-ofdirectory4 string Output directory
"-translationoutseq" associated qualifiers
-osformat5 string Output seq format
-osextension5 string File name extension
-osname5 string Base file name
-osdirectory5 string Output directory
-osdbname5 string Database name to add
-ossingle5 boolean Separate file for each entry
-oufo5 string UFO features
-offormat5 string Features format
-ofname5 string Features file name
-ofdirectory5 string Output directory
"-restoutseq" associated qualifiers
-osformat6 string Output seq format
-osextension6 string File name extension
-osname6 string Base file name
-osdirectory6 string Output directory
-osdbname6 string Database name to add
-ossingle6 boolean Separate file for each entry
-oufo6 string UFO features
-offormat6 string Features format
-ofname6 string Features file name
-ofdirectory6 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>[-seqall]<br>(Parameter 1)</td>
<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.coderet</td>
</tr>
<tr>
<td>[-cdsoutseq]<br>(Parameter 3)</td>
<td>Coding nucleotide output sequence(s) (optional)</td>
<td>Writeable sequence(s)</td>
<td><i><*></i>.<i>format</i></td>
</tr>
<tr>
<td>[-mrnaoutseq]<br>(Parameter 4)</td>
<td>Messenger RNA nucleotide output sequence(s) (optional)</td>
<td>Writeable sequence(s)</td>
<td><i><*></i>.<i>format</i></td>
</tr>
<tr>
<td>[-translationoutseq]<br>(Parameter 5)</td>
<td>Translated coding protein output sequence(s) (optional)</td>
<td>Writeable sequence(s)</td>
<td><i><*></i>.<i>format</i></td>
</tr>
<tr>
<td>[-restoutseq]<br>(Parameter 6)</td>
<td>Non-coding nucleotide output sequence(s) (optional)</td>
<td>Writeable sequence(s)</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 colspan=4>(none)</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>coderet</b> reads one or more nucleic sequence USAs having CDS, mRNA
or translation headings in their feature tables.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:x03487' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:x03487</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID X03487; SV 1; linear; genomic DNA; STD; HUM; 512 BP.
XX
AC X03487;
XX
DT 02-JUL-1986 (Rel. 09, Created)
DT 24-AUG-2005 (Rel. 84, Last updated, Version 3)
XX
DE Human apoferritin H gene exon 1
XX
KW ferritin.
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 1-512
RX DOI; 10.1093/nar/14.2.721.
RX PUBMED; 3003694.
RA Costanzo F., Colombo M., Staempfli S., Santoro C., Marone M., Frank R.,
RA Delius H., Cortese R.;
RT "Structure of gene and pseudogenes of human apoferritin H";
RL Nucleic Acids Res. 14(2):721-736(1986).
XX
DR EPD; EP11112; HS_FTH1.
DR RFAM; RF00037.
XX
FH Key Location/Qualifiers
FH
FT source 1..512
FT /organism="Homo sapiens"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:9606"
FT misc_feature 65..70
FT /note="GGGCGG box"
FT misc_feature 103..108
FT /note="GGGCGG box"
FT misc_feature 126..131
FT /note="GGGCGG box"
FT promoter 150..154
FT /note="put. TATA box"
FT mRNA 179..500
FT /note="exon 1"
FT CDS join(387..500,X03488.1:50..196,X03488.1:453..578,
FT X03488.1:674..838)
FT /product="apoferritin H subunit"
FT /db_xref="GDB:120617"
FT /db_xref="GOA:P02794"
FT /db_xref="HGNC:3976"
FT /db_xref="InterPro:IPR001519"
FT /db_xref="InterPro:IPR008331"
FT /db_xref="InterPro:IPR009040"
FT /db_xref="InterPro:IPR009078"
FT /db_xref="InterPro:IPR012347"
FT /db_xref="PDB:1FHA"
FT /db_xref="PDB:2FHA"
FT /db_xref="UniProtKB/Swiss-Prot:P02794"
FT /protein_id="CAA27205.1"
FT /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRD
FT DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECA
FT LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPE
FT SGLAEYLFDKHTLGDSDNES"
FT intron 501..>512
FT /note="intron I"
XX
SQ Sequence 512 BP; 80 A; 212 C; 152 G; 64 T; 4 other;
agnncaaacc tnagctccgc cagagcgcgc gaggcctcca gcggccgccc ctcccccaca 60
gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt 120
ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca 180
gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg 240
gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg 300
caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc 360
gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga 420
actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct 480
cctacgttta cctgtccatg gtgagcgcgg gc 512
//
</pre>
</td></tr></table><p>
<a name="input.2"></a>
<h3>Input files for usage example 2</h3>
<p><h3>Database entry: tembl:X03487</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID X03487; SV 1; linear; genomic DNA; STD; HUM; 512 BP.
XX
AC X03487;
XX
DT 02-JUL-1986 (Rel. 09, Created)
DT 24-AUG-2005 (Rel. 84, Last updated, Version 3)
XX
DE Human apoferritin H gene exon 1
XX
KW ferritin.
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 1-512
RX DOI; 10.1093/nar/14.2.721.
RX PUBMED; 3003694.
RA Costanzo F., Colombo M., Staempfli S., Santoro C., Marone M., Frank R.,
RA Delius H., Cortese R.;
RT "Structure of gene and pseudogenes of human apoferritin H";
RL Nucleic Acids Res. 14(2):721-736(1986).
XX
DR EPD; EP11112; HS_FTH1.
DR RFAM; RF00037.
XX
FH Key Location/Qualifiers
FH
FT source 1..512
FT /organism="Homo sapiens"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:9606"
FT misc_feature 65..70
FT /note="GGGCGG box"
FT misc_feature 103..108
FT /note="GGGCGG box"
FT misc_feature 126..131
FT /note="GGGCGG box"
FT promoter 150..154
FT /note="put. TATA box"
FT mRNA 179..500
FT /note="exon 1"
FT CDS join(387..500,X03488.1:50..196,X03488.1:453..578,
FT X03488.1:674..838)
FT /product="apoferritin H subunit"
FT /db_xref="GDB:120617"
FT /db_xref="GOA:P02794"
FT /db_xref="HGNC:3976"
FT /db_xref="InterPro:IPR001519"
FT /db_xref="InterPro:IPR008331"
FT /db_xref="InterPro:IPR009040"
FT /db_xref="InterPro:IPR009078"
FT /db_xref="InterPro:IPR012347"
FT /db_xref="PDB:1FHA"
FT /db_xref="PDB:2FHA"
FT /db_xref="UniProtKB/Swiss-Prot:P02794"
FT /protein_id="CAA27205.1"
FT /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRD
FT DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECA
FT LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPE
FT SGLAEYLFDKHTLGDSDNES"
FT intron 501..>512
FT /note="intron I"
XX
SQ Sequence 512 BP; 80 A; 212 C; 152 G; 64 T; 4 other;
agnncaaacc tnagctccgc cagagcgcgc gaggcctcca gcggccgccc ctcccccaca 60
gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt 120
ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca 180
gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg 240
gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg 300
caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc 360
gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga 420
actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct 480
cctacgttta cctgtccatg gtgagcgcgg gc 512
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
The output is a sequence file containing any CDS, mRNA and protein
translation sequences as specified by the feature table of the sequence(s).
<p>
One or more of CDS, mRNA, translation can be excluded from the output by
using the appropriate qualifiers to the program (i.e. <b>-nocds</b>,
etc.)
<p>
The ID names of the output sequences are constructed from the name of
the input sequence, the type of feature being output (i.e. <b>cds</b>,
<b>mrna</b>, <b>pro</b>) and a unique ordinal number for this type to
distinguish it from others in this sequence. The name, type and number
of separated by underscore characters. Thus the second CDS feature in
the sequence 'HSXYZ' would be named 'HSXYZ_cds_2'.
<p>
The translations are not made from the coding sequence, they are extracted
directly from the translation sequence held in the feature table.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: x03487.cds</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>x03487_cds_1
atgacgaccgcgtccacctcgcaggtgcgccagaactaccaccaggactcagaggccgcc
atcaaccgccagatcaacctggagctctacgcctcctacgtttacctgtccatgtcttac
tactttgaccgcgatgatgtggctttgaagaactttgccaaatactttcttcaccaatct
catgaggagagggaacatgctgagaaactgatgaagctgcagaaccaacgaggtggccga
atcttccttcaggatatcaagaaaccagactgtgatgactgggagagcgggctgaatgca
atggagtgtgcattacatttggaaaaaaatgtgaatcagtcactactggaactgcacaaa
ctggccactgacaaaaatgacccccatttgtgtgacttcattgagacacattacctgaat
gagcaggtgaaagccatcaaagaattgggtgaccacgtgaccaacttgcgcaagatggga
gcgcccgaatctggcttggcggaatatctctttgacaagcacaccctgggagacagtgat
aatgaaagctaa
</pre>
</td></tr></table><p>
<p><h3>File: x03487.mrna</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>x03487_mrna_1
cagacgttcttcgccgagagtcgtcggggtttcctgcttcaacagtgcttggacggaacc
cggcgctcgttccccaccccggccggccgcccatagccagccctccgtcgacctcttcac
cgcaccctcggactgccccaaggcccccgccgccgctccagcgccgcgcagccaccgccg
ccgccgccgcctctccttagtcgccgccatgacgaccgcgtccacctcgcaggtgcgcca
gaactaccaccaggactcagaggccgccatcaaccgccagatcaacctggagctctacgc
ctcctacgtttacctgtccatg
</pre>
</td></tr></table><p>
<p><h3>File: x03487.prot</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>x03487_pro_1
MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS
HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHK
LATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSD
NES
</pre>
</td></tr></table><p>
<p><h3>File: x03487.noncoding</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>x03487_noncoding_1
agnncaaacctnagctccgccagagcgcgcgaggcctccagcggccgcccctcccccaca
gcaggggcggggntcccgcgcccaccggaaggagcgggctcggggcgggcggcgctgatt
ggccggggcgggcctgacgccgacgcggctataagagaccacaagcgacccgcagggc
>x03487_noncoding_501
gtgagcgcgggc
</pre>
</td></tr></table><p>
<p><h3>File: x03487.coderet</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
CDS mRNA non-c Trans Total Sequence
===== ===== ===== ===== ===== ========
1 1 2 1 5 X03487
</pre>
</td></tr></table><p>
<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: x03487.coderet</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
mRNA Total Sequence
===== ===== ========
1 1 X03487
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
The translations are not made from the coding sequence, they are extracted
directly from the translation sequence held in the feature table.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 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="backtranambig.html">backtranambig</a></td>
<td>Back translate a protein sequence to ambiguous codons</td>
</tr>
<tr>
<td><a href="backtranseq.html">backtranseq</a></td>
<td>Back translate a protein sequence</td>
</tr>
<tr>
<td><a href="extractfeat.html">extractfeat</a></td>
<td>Extract features from a sequence</td>
</tr>
<tr>
<td><a href="maskfeat.html">maskfeat</a></td>
<td>Mask off features of a sequence</td>
</tr>
<tr>
<td><a href="plotorf.html">plotorf</a></td>
<td>Plot potential open reading frames</td>
</tr>
<tr>
<td><a href="prettyseq.html">prettyseq</a></td>
<td>Output sequence with translated ranges</td>
</tr>
<tr>
<td><a href="remap.html">remap</a></td>
<td>Display sequence with restriction sites, translation etc</td>
</tr>
<tr>
<td><a href="showfeat.html">showfeat</a></td>
<td>Show features of a sequence</td>
</tr>
<tr>
<td><a href="showorf.html">showorf</a></td>
<td>Pretty output of DNA translations</td>
</tr>
<tr>
<td><a href="showseq.html">showseq</a></td>
<td>Display a sequence with features, translation etc</td>
</tr>
<tr>
<td><a href="sixpack.html">sixpack</a></td>
<td>Display a DNA sequence with 6-frame translation and ORFs</td>
</tr>
<tr>
<td><a href="transeq.html">transeq</a></td>
<td>Translate nucleic acid sequences</td>
</tr>
<tr>
<td><a href="twofeat.html">twofeat</a></td>
<td>Finds neighbouring pairs of features in sequences</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Written (Nov 2000) - Alan Bleasby.
<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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