pasteseq Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Insert one sequence into another Description 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 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 Insert one sequence into another Version: EMBOSS:6.4.0.0 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 [.] Sequence filename and optional format (output 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 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 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 18-MAY-2010, entry version 81. DE RecName: Full=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] DR GeneID; 880573; -. DR GenomeReviews; AE004091_GR; PA3363. DR KEGG; pae:PA3363; -. DR PseudoCAP; PA3363; -. DR HOGENOM; HBG638444; -. DR OMA; QLQRIGC; -. DR ProtClustDB; CLSK867929; -. DR BioCyc; PAER208964:PA3363-MONOMER; -. DR GO; GO:0006350; P:transcription; IEA:UniProtKB-KW. DR GO; GO:0031564; P:transcription antitermination; IEA:UniProtKB-KW. DR InterPro; IPR005561; AmiR_NasR_reg. DR InterPro; IPR011006; CheY-like. DR InterPro; IPR008327; Sig_transdc_resp-reg_antiterm. DR InterPro; IPR011991; WHTH_trsnscrt_rep_DNA-bd. DR Gene3D; G3DSA:1.10.10.10; Wing_hlx_DNA_bd; 1. DR Pfam; PF03861; ANTAR; 1. DR PIRSF; PIRSF036382; RR_antiterm; 1. DR SUPFAM; SSF52172; CheY_like; 1. DR PROSITE; PS50921; ANTAR; 1. PE 1: Evidence at protein level; 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; 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 // 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 // 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 Reads and writes alignments aligncopypair Reads and writes pairs from alignments biosed Replace or delete sequence sections codcopy Copy and reformat a codon usage table cutseq Removes a section from a sequence degapseq Removes non-alphabetic (e.g. gap) characters from sequences descseq Alter the name or description of a sequence entret Retrieves 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 Reads and writes a feature table featreport Reads and writes 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 Masks all ambiguity characters in nucleotide sequences with N maskambigprot Masks 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 Reads and writes (returns) one set of sequences from many revseq Reverse and complement a nucleotide sequence seqcount Reads and counts sequences seqret Reads and writes (returns) sequences seqretsetall Reads and writes (returns) many sets of sequences seqretsplit Reads sequences and writes them to individual files sizeseq Sort sequences by size skipredundant Remove redundant sequences from an input set skipseq Reads and writes (returns) 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 Removes 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 (c) emboss.open-bio.org) not to the original author. 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