|   | biosed | 
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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
| 
Replace or delete sequence sections
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
   -targetregion       string     [N] Sequence section to match (Any string)
*  -replace            string     [A] Replacement sequence section (Any
                                  string)
  [-outseq]            seqout     [ | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) | seqall | (Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| -targetregion | string | Sequence section to match | Any string | N | 
| -replace | string | Replacement sequence section | Any string | A | 
| [-outseq] (Parameter 2) | seqout | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format | 
| Additional (Optional) qualifiers | ||||
| -position | integer | Sequence position to match | Integer 0 or more | 0 | 
| Advanced (Unprompted) qualifiers | ||||
| -delete | toggle | Delete the target sequence sections | Toggle value Yes/No | No | 
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0 | 
| -send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0 | 
| -sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N | 
| -sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | 
| -snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N | 
| -sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N | 
| -slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N | 
| -supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N | 
| -scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N | 
| -squick1 -squick_sequence | boolean | Read id and sequence only | Boolean value Yes/No | N | 
| -sformat1 -sformat_sequence | string | Input sequence format | Any string | |
| -iquery1 -iquery_sequence | string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0 | 
| -sdbname1 -sdbname_sequence | string | Database name | Any string | |
| -sid1 -sid_sequence | string | Entryname | Any string | |
| -ufo1 -ufo_sequence | string | UFO features | Any string | |
| -fformat1 -fformat_sequence | string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence | string | Features file name | Any string | |
| "-outseq" associated seqout qualifiers | ||||
| -osformat2 -osformat_outseq | string | Output seq format | Any string | |
| -osextension2 -osextension_outseq | string | File name extension | Any string | |
| -osname2 -osname_outseq | string | Base file name | Any string | |
| -osdirectory2 -osdirectory_outseq | string | Output directory | Any string | |
| -osdbname2 -osdbname_outseq | string | Database name to add | Any string | |
| -ossingle2 -ossingle_outseq | boolean | Separate file for each entry | Boolean value Yes/No | N | 
| -oufo2 -oufo_outseq | string | UFO features | Any string | |
| -offormat2 -offormat_outseq | string | Features format | Any string | |
| -ofname2 -ofname_outseq | string | Features file name | Any string | |
| -ofdirectory2 -ofdirectory_outseq | string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | 
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | 
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | 
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | 
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | 
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | 
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | 
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | 
| -error | boolean | Report errors | Boolean value Yes/No | Y | 
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | 
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | 
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | 
| 
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 INSDC.
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 sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
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="H-InvDB:HIT000322806.14"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="PDB:2L7R"
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   16-MAY-2012, entry version 93.
DE   RecName: Full=Aliphatic amidase regulator;
GN   Name=amiR; OrderedLocusNames=PA3363;
OS   Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG
OS   12228).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
OX   NCBI_TaxID=208964;
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
  [Part of this file has been deleted for brevity]
DR   eggNOG; COG3707; -.
DR   HOGENOM; HOG000247749; -.
DR   OMA; QRIGCQV; -.
DR   ProtClustDB; CLSK867929; -.
DR   BioCyc; PAER208964:PA3363-MONOMER; -.
DR   EvolutionaryTrace; P10932; -.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0031564; P:transcription antitermination; IEA:UniProtKB-KW.
DR   GO; GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW.
DR   Gene3D; G3DSA:1.10.10.10; Wing_hlx_DNA_bd; 1.
DR   InterPro; IPR005561; ANTAR.
DR   InterPro; IPR011006; CheY-like_superfamily.
DR   InterPro; IPR008327; Sig_transdc_resp-reg_antiterm.
DR   InterPro; IPR011991; WHTH_trsnscrt_rep_DNA-bd.
DR   Pfam; PF03861; ANTAR; 1.
DR   PIRSF; PIRSF036382; RR_antiterm; 1.
DR   SMART; SM01012; ANTAR; 1.
DR   SUPFAM; SSF52172; CheY_like; 1.
DR   PROSITE; PS50921; ANTAR; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Complete proteome; Reference 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; CAA32023).
FT   CONFLICT     64     64       R -> G (in Ref. 1; CAA32023).
FT   CONFLICT    141    141       E -> D (in Ref. 1; CAA32023).
FT   CONFLICT    154    154       A -> V (in Ref. 1; CAA32023).
FT   CONFLICT    170    170       Y -> H (in Ref. 1; CAA32023).
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.
| Program name | Description | 
|---|---|
| aligncopy | Read and write alignments | 
| aligncopypair | Read and write pairs from alignments | 
| 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 | 
| maskfeat | Write a sequence with masked features | 
| 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 | 
| 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 | 
| 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 | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.