                                   biosed



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Function

   Replace or delete sequence sections

Description

   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.

Algorithm

   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.

Usage

   Here is a sample session with biosed

   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

Command line arguments

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     [.] 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   It reads the USA of one or more nucleic acid or protein sequences.

  Input files for usage example

   'tembl:x65923' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:x65923

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
//

  Input files for usage example 2

   'tsw:amir_pseae' is a sequence entry in the example protein database
   'tsw'

  Database entry: tsw:amir_pseae

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
//

Output file format

   The edited sequence is output.

   The sequence will be in uppercase.

  Output files for usage example

  File: x65923.rna

>X65923 X65923.1 H.sapiens fau mRNA
UUCCUCUUUCUCGACUCCAUCUUCGCGGUAGCUGGGACCGCCGUUCAGUCGCCAAUAUGC
AGCUCUUUGUCCGCGCCCAGGAGCUACACACCUUCGAGGUGACCGGCCAGGAAACGGUCG
CCCAGAUCAAGGCUCAUGUAGCCUCACUGGAGGGCAUUGCCCCGGAAGAUCAAGUCGUGC
UCCUGGCAGGCGCGCCCCUGGAGGAUGAGGCCACUCUGGGCCAGUGCGGGGUGGAGGCCC
UGACUACCCUGGAAGUAGCAGGCCGCAUGCUUGGAGGUAAAGUUCAUGGUUCCCUGGCCC
GUGCUGGAAAAGUGAGAGGUCAGACUCCUAAGGUGGCCAAACAGGAGAAGAAGAAGAAGA
AGACAGGUCGGGCUAAGCGGCGGAUGCAGUACAACCGGCGCUUUGUCAACGUUGUGCCCA
CCUUUGGCAAGAAGAAGGGCCCCAAUGCCAACUCUUAAGUCUUUUGUAAUUCUGGCUUUC
UCUAAUAAAAAAGCCACUUAGUUCAGUCAAAAAAAAAA

  Output files for usage example 2

  File: amir_pseae.pep

>AMIR_PSEAE P10932 Aliphatic amidase regulator
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWXXPPPXXESFDVPVDVV
FTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVL
PVLVSARRISEEMAKLKQKTEQLQERIAGQARINQAKALLMQRHGWDEREAHQYLSREAM
KRREPILKIAQELLGNEPSA

Data files

   None.

Notes

   biosed was inspired by the useful UNIX utility sed which searches for a
   pattern in text and can replace or delete the found pattern.

References

   None.

Warnings

   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.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   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

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Written (Jan 2002) - Alan Bleasby

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
