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pasteseq |
Wiki
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Function
Insert one sequence into anotherDescription
pasteseq inserts one sequence into another at a specified position and writes the new, combined sequence to an output file.
Usage
Here is a sample session with pasteseqTo 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
Insert one sequence into another
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-asequence] sequence (Gapped) sequence filename and optional
format, or reference (input USA)
[-bsequence] sequence Sequence to insert
-pos integer [$(asequence.end)] The position in the main
input sequence to insert after.
To insert before the start use the position
0. (Integer 0 or more)
[-outseq] seqout [
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-asequence] (Parameter 1) |
sequence | (Gapped) sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-bsequence] (Parameter 2) |
sequence | Sequence to insert | Readable sequence | Required |
| -pos | integer | 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) |
seqout | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-asequence" associated sequence qualifiers | ||||
| -sbegin1 -sbegin_asequence |
integer | Start of the sequence to be used | Any integer value | 0 |
| -send1 -send_asequence |
integer | End of the sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_asequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_asequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_asequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_asequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_asequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_asequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -scircular1 -scircular_asequence |
boolean | Sequence is circular | Boolean value Yes/No | N |
| -squick1 -squick_asequence |
boolean | Read id and sequence only | Boolean value Yes/No | N |
| -sformat1 -sformat_asequence |
string | Input sequence format | Any string | |
| -iquery1 -iquery_asequence |
string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_asequence |
integer | Input start position offset | Any integer value | 0 |
| -sdbname1 -sdbname_asequence |
string | Database name | Any string | |
| -sid1 -sid_asequence |
string | Entryname | Any string | |
| -ufo1 -ufo_asequence |
string | UFO features | Any string | |
| -fformat1 -fformat_asequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_asequence |
string | Features file name | Any string | |
| "-bsequence" associated sequence qualifiers | ||||
| -sbegin2 -sbegin_bsequence |
integer | Start of the sequence to be used | Any integer value | 0 |
| -send2 -send_bsequence |
integer | End of the sequence to be used | Any integer value | 0 |
| -sreverse2 -sreverse_bsequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask2 -sask_bsequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide2 -snucleotide_bsequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein2 -sprotein_bsequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower2 -slower_bsequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper2 -supper_bsequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -scircular2 -scircular_bsequence |
boolean | Sequence is circular | Boolean value Yes/No | N |
| -squick2 -squick_bsequence |
boolean | Read id and sequence only | Boolean value Yes/No | N |
| -sformat2 -sformat_bsequence |
string | Input sequence format | Any string | |
| -iquery2 -iquery_bsequence |
string | Input query fields or ID list | Any string | |
| -ioffset2 -ioffset_bsequence |
integer | Input start position offset | Any integer value | 0 |
| -sdbname2 -sdbname_bsequence |
string | Database name | Any string | |
| -sid2 -sid_bsequence |
string | Entryname | Any string | |
| -ufo2 -ufo_bsequence |
string | UFO features | Any string | |
| -fformat2 -fformat_bsequence |
string | Features format | Any string | |
| -fopenfile2 -fopenfile_bsequence |
string | Features file name | Any string | |
| "-outseq" associated seqout qualifiers | ||||
| -osformat3 -osformat_outseq |
string | Output seq format | Any string | |
| -osextension3 -osextension_outseq |
string | File name extension | Any string | |
| -osname3 -osname_outseq |
string | Base file name | Any string | |
| -osdirectory3 -osdirectory_outseq |
string | Output directory | Any string | |
| -osdbname3 -osdbname_outseq |
string | Database name to add | Any string | |
| -ossingle3 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N |
| -oufo3 -oufo_outseq |
string | UFO features | Any string | |
| -offormat3 -offormat_outseq |
string | Features format | Any string | |
| -ofname3 -ofname_outseq |
string | Features file name | Any string | |
| -ofdirectory3 -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 |
Input file format
pasteseq reads two nucleotide or protein sequences.
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
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 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
//
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Database entry: tsw:flav_nossm
ID FLAV_NOSSM Reviewed; 35 AA.
AC P35707;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 1.
DT 19-JAN-2010, entry version 39.
DE RecName: Full=Flavodoxin;
DE Flags: Fragment;
OS Nostoc sp. (strain MAC).
OC Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Nostoc.
OX NCBI_TaxID=35822;
RN [1]
RP PROTEIN 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.
CC -!- SIMILARITY: Contains 1 flavodoxin-like 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 GO; GO:0009055; F:electron carrier activity; IEA:InterPro.
DR GO; GO:0010181; F:FMN binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR GO; GO:0022900; P:electron transport chain; IEA:UniProtKB-KW.
DR GO; GO:0006810; P:transport; IEA:UniProtKB-KW.
DR InterPro; IPR008254; Flavodoxin/NO_synth.
DR InterPro; IPR001226; Flavodoxin_CS.
DR PROSITE; PS00201; FLAVODOXIN; 1.
DR PROSITE; PS50902; FLAVODOXIN_LIKE; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; Electron transport; Flavoprotein; FMN;
KW Transport.
FT CHAIN 1 >35 Flavodoxin.
FT /FTId=PRO_0000171640.
FT DOMAIN 4 >35 Flavodoxin-like.
FT NON_TER 35 35
SQ SEQUENCE 35 AA; 3820 MW; B6EEB5CA7A45DDA6 CRC64;
SKKIGLFYGT ZTGKTESVAE IIDEFGDEVV TLDID
//
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Output file format
The output is a standard EMBOSS sequence file.
The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
Output files for usage example
File: amir_pseae.fasta
>AMIR_PSEAE Aliphatic amidase regulator MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA |
Output files for usage example 2
File: amirplus.seq
>AMIR_PSEAE Aliphatic amidase regulator MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA |
Output files for usage example 3
File: amirplus.seq
>AMIR_PSEAE Aliphatic amidase regulator SKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDMSANSLLGSLRELQVLVLNPPGEVS DALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVAL VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA |
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.See also
| Program name | Description |
|---|---|
| aligncopy | Read and write alignments |
| aligncopypair | Read and write pairs from alignments |
| biosed | Replace or delete sequence sections |
| 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 |
| 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)
Gary Williams formerly at:MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.