| biosed

## 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 a specified second subsequence (or optionally just deletes the found target subsequence).

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

If the target subsequence occurs more than once, then each instance of the target is replaced.

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.

## 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

       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

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

## 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 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
    //

### 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   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.
    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
    //

## 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

The edited sequence will be output in uppercase.

## References

None.

## Warnings

No check is made on the replacement subsequence.
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.

## Diagnostic Error Messages

None.

## Exit status