EMBOSS: pasteseq manual

pasteseq

Function

Insert one sequence into another

Description

This simple editing program allows you to insert one sequence into another sequence after a specified position and to then write out the results to a sequence file.

Usage

Here is a sample session with pasteseq

To insert the sequence 'tsw:flav_nossm' after position 67 in sequence 'tsw:amir_pseae' and write the results to the file 'amir_pseae.fasta':


% pasteseq tsw:amir_pseae tsw:flav_nossm -pos=67 
Insert one sequence into another
Output sequence [amir_pseae.fasta]:

Go to the input files for this example
Go to the output files for this example

Example 2

This does the same thing, but the output qualifier is explicitly used:


% pasteseq tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=67 
Insert one sequence into another

Go to the output files for this example

Example 3

To insert the sequence 'tsw:flav_nossm' before the start of sequence 'tsw:amir_pseae' use -pos=0:


% pasteseq tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=0 
Insert one sequence into another

Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Sequence USA
  [-bsequence]         sequence   Sequence to insert
   -pos                integer    The position in the main input sequence to
                                  insert after.
                                  To insert before the start use the position
                                  0.
  [-outseq]            seqout     Output sequence USA

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-asequence" associated qualifiers
   -sbegin1             integer    Start of the sequence to be used
   -send1               integer    End of the 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

   "-bsequence" associated qualifiers
   -sbegin2             integer    Start of the sequence to be used
   -send2               integer    End of the sequence to be used
   -sreverse2           boolean    Reverse (if DNA)
   -sask2               boolean    Ask for begin/end/reverse
   -snucleotide2        boolean    Sequence is nucleotide
   -sprotein2           boolean    Sequence is protein
   -slower2             boolean    Make lower case
   -supper2             boolean    Make upper case
   -sformat2            string     Input sequence format
   -sdbname2            string     Database name
   -sid2                string     Entryname
   -ufo2                string     UFO features
   -fformat2            string     Features format
   -fopenfile2          string     Features file name

   "-outseq" associated qualifiers
   -osformat3           string     Output seq format
   -osextension3        string     File name extension
   -osname3             string     Base file name
   -osdirectory3        string     Output directory
   -osdbname3           string     Database name to add
   -ossingle3           boolean    Separate file for each entry
   -oufo3               string     UFO features
   -offormat3           string     Features format
   -ofname3             string     Features file name
   -ofdirectory3        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 deaths

Standard (Mandatory) qualifiers		Allowed values	Default
[-asequence] (Parameter 1)	Sequence USA	Readable sequence	Required
[-bsequence] (Parameter 2)	Sequence to insert	Readable sequence	Required
-pos	The position in the main input sequence to insert after. To insert before the start use the position 0.	Integer 0 or more	$(asequence.end)
[-outseq] (Parameter 3)	Output sequence USA	Writeable sequence	<sequence>.format
Additional (Optional) qualifiers		Allowed values	Default
(none)
Advanced (Unprompted) qualifiers		Allowed values	Default
(none)

Input file format

pasteseq reads 2 normal sequence USAs.

Input files for usage example

'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
//

Database entry: tsw:flav_nossm

ID   FLAV_NOSSM     STANDARD;      PRT;    35 AA.
AC   P35707;
DT   01-JUN-1994 (Rel. 29, Created)
DT   01-JUN-1994 (Rel. 29, Last sequence update)
DT   15-DEC-1998 (Rel. 37, Last annotation update)
DE   FLAVODOXIN (FRAGMENT).
OS   Nostoc sp. (strain MAC).
OC   Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Nostoc.
RN   [1]
RP   SEQUENCE.
RA   Takruri I.A.H., Boulter D., Fitzgerald M.P., Hutber G.N., Rogers L.J.;
RT   "N-terminal amino acid sequences of flavodoxins from Chondrus crispus
RT   and Nostoc strain MAC.";
RL   Phytochemistry 25:2113-2115(1986).
CC   -!- FUNCTION: LOW-POTENTIAL ELECTRON DONOR TO A NUMBER OF REDOX
CC       ENZYMES.
CC   -!- COFACTOR: FMN.
CC   -!- SIMILARITY: BELONGS TO THE FLAVODOXIN FAMILY.
DR   PIR; PA0004; PA0004.
DR   HSSP; P11241; 1RCF.
DR   INTERPRO; IPR001226; -.
DR   PFAM; PF00258; flavodoxin; 1.
DR   PROSITE; PS00201; FLAVODOXIN; 1.
KW   Electron transport; Flavoprotein; FMN.
FT   NON_TER      35     35
SQ   SEQUENCE   35 AA;  3820 MW;  B6EEB5CA7A45DDA6 CRC64;
     SKKIGLFYGT ZTGKTESVAE IIDEFGDEVV TLDID
//

Output file format

pasteseq writes a normal sequence file.

Output files for usage example

File: amir_pseae.fasta

>AMIR_PSEAE ALIPHATIC AMIDASE REGULATOR.
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSI
FQNGHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL
VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAG
QARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA

Output files for usage example 2

File: amirplus.seq

>AMIR_PSEAE ALIPHATIC AMIDASE REGULATOR.
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSI
FQNGHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL
VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAG
QARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA

Output files for usage example 3

File: amirplus.seq

>AMIR_PSEAE ALIPHATIC AMIDASE REGULATOR.
SKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDMSANSLLGSLRELQVLVLNPPGEVS
DALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVAL
VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAG
QARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA

Data files

None.

Notes

This can be used as a simple sequence editor.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
biosed	Replace or delete sequence sections
codcopy	Reads and writes a codon usage table
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	Write 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	Exclude a set of sequences and write out the remaining ones
nthseq	Writes one sequence from a multiple set of sequences
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 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)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Completed 26 Jan 1999

Target users

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

Comments

None

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tsw:amir_pseae

Database entry: tsw:flav_nossm

Output file format

Output files for usage example

File: amir_pseae.fasta

Output files for usage example 2

File: amirplus.seq

Output files for usage example 3

File: amirplus.seq

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments