|   | biosed | 
biosed is a simple sequence editing utility that searches for a target subsequence in one or more input sequences and replaces it with an insert subsequence, or optionally, just deletes the target subsequence where found. If the target subsequence occurs more than once, then each instance of the target is replaced or deleted.
The -position option allows a sequence position to be specified as an additional constraint for the match: a replacement / deletion only occurs if the start of a match is at the specified -position position.The target subsequence is just a short, literal sequence of characters. biosed cannot interpret cannot any sort of an ambiguity pattern such as a regular expression. A simple string match is done between the target and input sequences. If there is an exact matches then the replacement or deletion is done. The matching is case insensitive, independent of the case of both the input sequences and target.
Replace all 'T's with 'U's to create an RNA sequence
| % biosed tembl:x65923 x65923.rna -target T -replace U Replace or delete sequence sections | 
Go to the input files for this example
Go to the output files for this example
Example 2
Replace all 'PPP' protein motifs with 'XXPPPXX'
| % biosed tsw:amir_pseae amir_pseae.pep -target PPP -replace XXPPPXX Replace or delete sequence sections | 
Go to the input files for this example
Go to the output files for this example
| 
   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     [ | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) | (Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| -target | Sequence section to match | Any string is accepted | N | 
| -replace | Replacement sequence section | Any string is accepted | A | 
| [-outseq] (Parameter 2) | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| -position | Sequence position to match | Integer 0 or more | 0 | 
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -delete | Delete the target sequence sections | Toggle value Yes/No | No | 
| 
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
//
 | 
| 
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
  [Part of this file has been deleted for brevity]
CC   -!- SIMILARITY: Contains 1 ANTAR domain.
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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
//
 | 
The sequence will be in uppercase.
| >X65923 X65923.1 H.sapiens fau mRNA UUCCUCUUUCUCGACUCCAUCUUCGCGGUAGCUGGGACCGCCGUUCAGUCGCCAAUAUGC AGCUCUUUGUCCGCGCCCAGGAGCUACACACCUUCGAGGUGACCGGCCAGGAAACGGUCG CCCAGAUCAAGGCUCAUGUAGCCUCACUGGAGGGCAUUGCCCCGGAAGAUCAAGUCGUGC UCCUGGCAGGCGCGCCCCUGGAGGAUGAGGCCACUCUGGGCCAGUGCGGGGUGGAGGCCC UGACUACCCUGGAAGUAGCAGGCCGCAUGCUUGGAGGUAAAGUUCAUGGUUCCCUGGCCC GUGCUGGAAAAGUGAGAGGUCAGACUCCUAAGGUGGCCAAACAGGAGAAGAAGAAGAAGA AGACAGGUCGGGCUAAGCGGCGGAUGCAGUACAACCGGCGCUUUGUCAACGUUGUGCCCA CCUUUGGCAAGAAGAAGGGCCCCAAUGCCAACUCUUAAGUCUUUUGUAAUUCUGGCUUUC UCUAAUAAAAAAGCCACUUAGUUCAGUCAAAAAAAAAA | 
| >AMIR_PSEAE P10932 Aliphatic amidase regulator. MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWXXPPPXXESFDVPVDVV FTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVL PVLVSARRISEEMAKLKQKTEQLQERIAGQARINQAKALLMQRHGWDEREAHQYLSREAM KRREPILKIAQELLGNEPSA | 
biosed was inspired by the useful UNIX utility sed which searches for a pattern in text and can replace or delete the found pattern.
No check for correct type (protein, nucleic, gapped etc) is made on the replacement sequence so you must ensure it is of the type required. Any text can be used, 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.