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|
<HTML>
<HEAD>
<TITLE>
EMBOSS: biosed
</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">
biosed
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Replace or delete sequence sections
<H2>
Description
</H2>
<b>biosed</b> is a simple sequence editing utility that searches for a
target subsequence in one or more input sequences and replaces it with a
specified second subsequence (or optionally just deletes the found
target subsequence).
<p>
<b>biosed</b> was inspired by the useful UNIX utility <b>sed</b> which
searches for a pattern in text and can replace or delete the found
pattern.
<p>
If the target subsequence occurs more than once, then each instance of
the target is replaced.
<p>
The target subsequence is not any sort of an ambiguity pattern, it is
just a short sequence. A simple string match is done and if it exactly
matches then the replacement is done. The matching is independent of
the case of the sequence or the target - both uppercase and lowercase
will match.
<H2>
Usage
</H2>
<b>Here is a sample session with biosed</b>
<p>
Replace all 'T's with 'U's to create an RNA sequence
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>biosed tembl:x65923 x65923.rna -target T -replace U </b>
Replace or delete sequence sections
</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>
Replace all 'PPP' protein motifs with 'XXPPPXX'
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>biosed tsw:amir_pseae amir_pseae.pep -target PPP -replace XXPPPXX </b>
Replace or delete sequence sections
</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 (* if not always prompted):
[-sequence] seqall (Gapped) sequence(s) filename and optional
format, or reference (input USA)
-target string [N] Sequence section to match (Any string is
accepted)
* -replace string [A] Replacement sequence section (Any string
is accepted)
[-outseq] seqout [<sequence>.<format>] Sequence filename and
optional format (output USA)
Additional (Optional) qualifiers:
-position integer [0] Sequence position to match (Integer 0 or
more)
Advanced (Unprompted) qualifiers:
-delete toggle [N] Delete the target sequence sections
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>(Gapped) sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-target</td>
<td>Sequence section to match</td>
<td>Any string is accepted</td>
<td>N</td>
</tr>
<tr>
<td>-replace</td>
<td>Replacement sequence section</td>
<td>Any string is accepted</td>
<td>A</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>-position</td>
<td>Sequence position to match</td>
<td>Integer 0 or more</td>
<td>0</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>-delete</td>
<td>Delete the target sequence sections</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>
</table>
<H2>
Input file format
</H2>
It reads the USA of one or more nucleic acid or protein sequences.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:x65923</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC X65923;
XX
DT 13-MAY-1992 (Rel. 31, Created)
DT 18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE H.sapiens fau mRNA
XX
KW fau gene.
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 1-518
RA Michiels L.M.R.;
RT ;
RL Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN [2]
RP 1-518
RX PUBMED; 8395683.
RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8(9):2537-2546(1993).
XX
DR H-InvDB; HIT000322806.
XX
FH Key Location/Qualifiers
FH
FT source 1..518
FT /organism="Homo sapiens"
FT /chromosome="11q"
FT /map="13"
FT /mol_type="mRNA"
FT /clone_lib="cDNA"
FT /clone="pUIA 631"
FT /tissue_type="placenta"
FT /db_xref="taxon:9606"
FT misc_feature 57..278
FT /note="ubiquitin like part"
FT CDS 57..458
FT /gene="fau"
FT /db_xref="GDB:135476"
FT /db_xref="GOA:P35544"
FT /db_xref="GOA:P62861"
FT /db_xref="HGNC:3597"
FT /db_xref="UniProtKB/Swiss-Prot:P35544"
FT /db_xref="UniProtKB/Swiss-Prot:P62861"
FT /protein_id="CAA46716.1"
FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT misc_feature 98..102
FT /note="nucleolar localization signal"
FT misc_feature 279..458
FT /note="S30 part"
FT polyA_signal 484..489
FT polyA_site 509
XX
SQ Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc 60
agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 120
cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 180
tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 240
tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 300
gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 360
agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 420
cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 480
tctaataaaa aagccactta gttcagtcaa aaaaaaaa 518
//
</pre>
</td></tr></table><p>
<a name="input.2"></a>
<h3>Input files for usage example 2</h3>
'tsw:amir_pseae' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:amir_pseae</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID AMIR_PSEAE Reviewed; 196 AA.
AC P10932;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 08-DEC-2000, sequence version 2.
DT 20-MAR-2007, entry version 55.
DE Aliphatic amidase regulator.
GN Name=amiR; OrderedLocusNames=PA3363;
OS Pseudomonas aeruginosa.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=PAC433;
RX MEDLINE=89211409; PubMed=2495988; DOI=10.1016/0014-5793(89)80249-2;
RA Lowe N., Rice P.M., Drew R.E.;
RT "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of
RT Pseudomonas aeruginosa.";
RL FEBS Lett. 246:39-43(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228;
RX MEDLINE=20437337; PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T.,
RA Reizer J., Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an
RT opportunistic pathogen.";
RL Nature 406:959-964(2000).
RN [3]
RP CHARACTERIZATION.
RX MEDLINE=95286483; PubMed=7539417;
RA Wilson S.A., Drew R.E.;
RT "Transcriptional analysis of the amidase operon from Pseudomonas
RT aeruginosa.";
RL J. Bacteriol. 177:3052-3057(1995).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF COMPLEX WITH AMIC.
RC STRAIN=PAC1;
RX MEDLINE=99437995; PubMed=10508151; DOI=10.1093/emboj/18.19.5175;
RA O'Hara B.P., Norman R.A., Wan P.T., Roe S.M., Barrett T.E., Drew R.E.,
RA Pearl L.H.;
RT "Crystal structure and induction mechanism of AmiC-AmiR: a ligand-
RT regulated transcription antitermination complex.";
RL EMBO J. 18:5175-5186(1999).
CC -!- FUNCTION: Positive controlling element of amiE, the gene for
CC aliphatic amidase. Acts as a transcriptional antitermination
<font color=red> [Part of this file has been deleted for brevity]</font>
CC -!- SIMILARITY: Contains 1 ANTAR domain.
CC -----------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution-NoDerivs License
CC -----------------------------------------------------------------------
DR EMBL; X13776; CAA32023.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG06751.1; -; Genomic_DNA.
DR PIR; B83226; B83226.
DR PIR; S03884; S03884.
DR PDB; 1QO0; X-ray; D/E=1-196.
DR IntAct; P10932; -.
DR GenomeReviews; AE004091_GR; PA3363.
DR KEGG; pae:PA3363; -.
DR BioCyc; PAER287:PA3363-MONOMER; -.
DR InterPro; IPR005561; AmiR_NasR_reg.
DR InterPro; IPR011006; CheY_like.
DR InterPro; IPR008327; Res_reg_antiterm.
DR Pfam; PF03861; ANTAR; 1.
DR PIRSF; PIRSF036382; RR_antiterm; 1.
DR PROSITE; PS50921; ANTAR; 1.
KW 3D-structure; Complete proteome; Transcription;
KW Transcription antitermination; Transcription regulation.
FT CHAIN 1 196 Aliphatic amidase regulator.
FT /FTId=PRO_0000064582.
FT DOMAIN 129 190 ANTAR.
FT CONFLICT 48 48 S -> A (in Ref. 1).
FT CONFLICT 64 64 R -> G (in Ref. 1).
FT CONFLICT 141 141 E -> D (in Ref. 1).
FT CONFLICT 154 154 A -> V (in Ref. 1).
FT CONFLICT 170 170 Y -> H (in Ref. 1).
FT HELIX 3 8
FT HELIX 9 12
FT STRAND 14 19
FT HELIX 23 35
FT STRAND 38 42
FT STRAND 54 59
FT HELIX 65 75
FT STRAND 81 86
FT HELIX 91 100
FT STRAND 103 109
FT HELIX 112 114
FT HELIX 115 160
FT HELIX 164 175
FT TURN 176 179
FT HELIX 182 189
SQ SEQUENCE 196 AA; 21903 MW; 306A4F30E8E4C6C0 CRC64;
MSANSLLGSL RELQVLVLNP PGEVSDALVL QLIRIGCSVR QCWPPPESFD VPVDVVFTSI
FQNRHHDEIA ALLAAGTPRT TLVALVEYES PAVLSQIIEL ECHGVITQPL DAHRVLPVLV
SARRISEEMA KLKQKTEQLQ ERIAGQARIN QAKALLMQRH GWDEREAHQY LSREAMKRRE
PILKIAQELL GNEPSA
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
The edited sequence is output.
<P>
The sequence will be in uppercase.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: x65923.rna</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>X65923 X65923.1 H.sapiens fau mRNA
UUCCUCUUUCUCGACUCCAUCUUCGCGGUAGCUGGGACCGCCGUUCAGUCGCCAAUAUGC
AGCUCUUUGUCCGCGCCCAGGAGCUACACACCUUCGAGGUGACCGGCCAGGAAACGGUCG
CCCAGAUCAAGGCUCAUGUAGCCUCACUGGAGGGCAUUGCCCCGGAAGAUCAAGUCGUGC
UCCUGGCAGGCGCGCCCCUGGAGGAUGAGGCCACUCUGGGCCAGUGCGGGGUGGAGGCCC
UGACUACCCUGGAAGUAGCAGGCCGCAUGCUUGGAGGUAAAGUUCAUGGUUCCCUGGCCC
GUGCUGGAAAAGUGAGAGGUCAGACUCCUAAGGUGGCCAAACAGGAGAAGAAGAAGAAGA
AGACAGGUCGGGCUAAGCGGCGGAUGCAGUACAACCGGCGCUUUGUCAACGUUGUGCCCA
CCUUUGGCAAGAAGAAGGGCCCCAAUGCCAACUCUUAAGUCUUUUGUAAUUCUGGCUUUC
UCUAAUAAAAAAGCCACUUAGUUCAGUCAAAAAAAAAA
</pre>
</td></tr></table><p>
<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: amir_pseae.pep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>AMIR_PSEAE P10932 Aliphatic amidase regulator.
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWXXPPPXXESFDVPVDVV
FTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVL
PVLVSARRISEEMAKLKQKTEQLQERIAGQARINQAKALLMQRHGWDEREAHQYLSREAM
KRREPILKIAQELLGNEPSA
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
The edited sequence will be output in uppercase.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
No check is made on the replacement subsequence.
<br>
Any text can be used as the replacement, including characters only used
in proteins (e.g. D, E, F, etc.), characters rarely used in proteins (e.g.
U, J, O, etc), digits and punctuation characters.
<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="codcopy.html">codcopy</a></td>
<td>Reads and writes a codon usage table</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="maskfeat.html">maskfeat</a></td>
<td>Mask off features of a sequence</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="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="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>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Written (Jan 2002) - 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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