| 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 a RNA sequence

    % biosed tembl:hsfau hsfau.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

       Mandatory qualifiers (* if not always prompted):
      [-sequence]          seqall     Sequence database USA
       -target             string     Sequence section to match
    *  -replace            string     Replacement sequence section
      [-outseq]            seqout     Output sequence USA

       Optional qualifiers: (none)
       Advanced qualifiers:
       -delete             boolean    Delete the target sequence sections

       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outseq" related 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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 deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database 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) | Output sequence USA | Writeable sequence | <sequence>.format
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-delete | Delete the target sequence sections | Boolean 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:hsfau' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:hsfau

    ID   HSFAU      standard; RNA; HUM; 518 BP.
    XX
    AC   X65923;
    XX
    SV   X65923.1
    XX
    DT   13-MAY-1992 (Rel. 31, Created)
    DT   23-SEP-1993 (Rel. 37, Last updated, Version 10)
    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; Primates; Catarrhini; Hominidae; 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   MEDLINE; 93368957.
    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 8:2537-2546(1993).
    XX
    DR   SWISS-PROT; P35544; UBIM_HUMAN.
    DR   SWISS-PROT; Q05472; RS30_HUMAN.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..518
    FT                   /chromosome="11q"
    FT                   /db_xref="taxon:9606"
    FT                   /organism="Homo sapiens"
    FT                   /tissue_type="placenta"
    FT                   /clone_lib="cDNA"
    FT                   /clone="pUIA 631"
    FT                   /map="13"
    FT   misc_feature    57..278
    FT                   /note="ubiquitin like part"
    FT   CDS             57..458
    FT                   /db_xref="SWISS-PROT:P35544"
    FT                   /db_xref="SWISS-PROT:Q05472"
    FT                   /gene="fau"
    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     STANDARD;      PRT;   196 AA.
    AC   P10932;
    DT   01-JUL-1989 (Rel. 11, Created)
    DT   01-JUL-1989 (Rel. 11, Last sequence update)
    DT   15-DEC-1998 (Rel. 37, Last annotation update)
    DE   ALIPHATIC AMIDASE REGULATOR.
    GN   AMIR.
    OS   Pseudomonas aeruginosa.
    OC   Bacteria; Proteobacteria; gamma subdivision; Pseudomonas group;
    OC   Pseudomonas.
    RN   [1]
    RP   SEQUENCE FROM N.A.
    RC   STRAIN=PAC;
    RX   MEDLINE; 89211409.
    RA   LOWE N., RICE P.M., DREW R.E.;
    RT   "Nucleotide sequence of the aliphatic amidase regulator gene (amiR)
    RT   of Pseudomonas aeruginosa.";
    RL   FEBS Lett. 246:39-43(1989).
    RN   [2]
    RP   CHARACTERIZATION.
    RX   MEDLINE; 95286483.
    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).
    CC   -!- FUNCTION: POSITIVE CONTROLLING ELEMENT OF AMIE, THE GENE FOR
    CC       ALIPHATIC AMIDASE. ACTS AS A TRANSCRIPTIONAL ANTITERMINATION
    CC       FACTOR. IT IS THOUGHT TO ALLOW RNA POLYMERASE READ THROUGH A RHO-
    CC       INDEPENDENT TRANSCRIPTION TERMINATOR BETWEEN THE AMIE PROMOTER AND
    CC       GENE.
    CC   --------------------------------------------------------------------------
    CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
    CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
    CC   the European Bioinformatics Institute.  There are no  restrictions on  its
    CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
    CC   modified and this statement is not removed.  Usage  by  and for commercial
    CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
    CC   or send an email to license@isb-sib.ch).
    CC   --------------------------------------------------------------------------
    DR   EMBL; X13776; CAA32023.1; -.
    DR   PIR; S03884; S03884.
    KW   Transcription regulation; Activator.
    SQ   SEQUENCE   196 AA;  21776 MW;  560A8AE3 CRC32;
         MSANSLLGSL RELQVLVLNP PGEVSDALVL QLIRIGCSVR QCWPPPEAFD VPVDVVFTSI
         FQNGHHDEIA ALLAAGTPRT TLVALVEYES PAVLSQIIEL ECHGVITQPL DAHRVLPVLV
         SARRISEEMA KLKQKTEQLQ DRIAGQARIN QAKVLLMQRH GWDEREAHQH LSREAMKRRE
         PILKIAQELL GNEPSA
    //

## Output file format

The edited sequence is output.

The sequence will be in uppercase.

### Output files for usage example

### File: hsfau.rna

    >HSFAU 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.
    MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWXXPPPXXEAFDVPVDVV
    FTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVL
    PVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAM
    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 not used in proteins (e.g. 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
--- | ---
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
listor | Writes a list file of the logical OR of two sets of sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads and writes (returns) sequences in individual files
skipseq | Reads and writes (returns) sequences, skipping the first few
splitter | Split a sequence into (overlapping) smaller sequences
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

## Author(s)

Alan Bleasby (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## 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