biosed 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 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 an insert subsequence, or optionally, just deletes the target subsequence where found. If the target subsequence occurs more than once, then each instance of the target is replaced or deleted. The -position option allows a sequence position to be specified as an additional constraint for the match: a replacement / deletion only occurs if the start of a match is at the specified -position position. Algorithm The target subsequence is just a short, literal sequence of characters. biosed cannot interpret cannot any sort of an ambiguity pattern such as a regular expression. A simple string match is done between the target and input sequences. If there is an exact matches then the replacement or deletion is done. The matching is case insensitive, independent of the case of both the input sequences and target. 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 Replace or delete sequence sections Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-sequence] seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) -targetregion string [N] Sequence section to match (Any string) * -replace string [A] Replacement sequence section (Any string) [-outseq] seqout [.] 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 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 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 sequence 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="InterPro:IPR000626" FT /db_xref="InterPro:IPR006846" FT /db_xref="InterPro:IPR019954" FT /db_xref="InterPro:IPR019955" FT /db_xref="InterPro:IPR019956" 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 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 // 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 biosed was inspired by the useful UNIX utility sed which searches for a pattern in text and can replace or delete the found pattern. References None. Warnings No check for correct type (protein, nucleic, gapped etc) is made on the replacement sequence so you must ensure it is of the type required. Any text can be used, 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 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 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 pasteseq Insert one sequence into another 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) Alan Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. 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 None