featmerge 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 Merge two overlapping feature tables Description featmerge reads two feature tables for the same sequence and combines them into a single table. Algorithm The second feature table is appended to the first, retaining the original order. Usage This run merges the GFF format output of one of the antigenic examples with the original feature table read from SwissProt. Here is a sample session with featmerge % featmerge Merge two overlapping feature tables Input feature table: tsw:actb1_takru Second input feature table: ../antigenic-keep/actb1_takru.antigenic Features output [actb1_takru.gff]: Go to the input files for this example Go to the output files for this example Command line arguments Merge two overlapping feature tables Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-afeatures] features (no help text) features value [-bfeatures] features (no help text) features value [-outfeat] featout [unknown.gff] Output features UFO Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-afeatures" associated qualifiers -fformat1 string Features format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -fopenfile1 string Features file name -fask1 boolean Prompt for begin/end/reverse -fbegin1 integer Start of the features to be used -fend1 integer End of the features to be used -freverse1 boolean Reverse (if DNA) -fcircular1 boolean Circular sequence features "-bfeatures" associated qualifiers -fformat2 string Features format -iquery2 string Input query fields or ID list -ioffset2 integer Input start position offset -fopenfile2 string Features file name -fask2 boolean Prompt for begin/end/reverse -fbegin2 integer Start of the features to be used -fend2 integer End of the features to be used -freverse2 boolean Reverse (if DNA) -fcircular2 boolean Circular sequence features "-outfeat" associated qualifiers -offormat3 string Output feature format -ofopenfile3 string Features file name -ofextension3 string File name extension -ofdirectory3 string Output directory -ofname3 string Base file name -ofsingle3 boolean Separate file for each entry 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 The input is a standard EMBOSS feaure query. Data can also be read from feaure output in any supported format format written by an EMBOSS application. featmerge reads two feature UFOs. Input files for usage example 'tsw:actb1_takru' is a sequence entry in the example protein database 'tsw' File: ../antigenic-keep/actb1_takru.antigenic ##gff-version 3 ##sequence-region ACTB1_TAKRU 1 375 #!Date 2013-07-15 #!Type Protein #!Source-version EMBOSS 6.6.0.0 ACTB1_TAKRU antigenic epitope 214 222 1.207 . . ID=ACTB1_TAKRU.1;note=*pos 218 ACTB1_TAKRU antigenic epitope 131 145 1.187 . . ID=ACTB1_TAKRU.2;note=*pos 137 ACTB1_TAKRU antigenic epitope 5 12 1.166 . . ID=ACTB1_TAKRU.3;note=*pos 8 ACTB1_TAKRU antigenic epitope 27 38 1.164 . . ID=ACTB1_TAKRU.4;note=*pos 32 ACTB1_TAKRU antigenic epitope 160 183 1.136 . . ID=ACTB1_TAKRU.5;note=*pos 173 ACTB1_TAKRU antigenic epitope 367 372 1.135 . . ID=ACTB1_TAKRU.6;note=*pos 372 ACTB1_TAKRU antigenic epitope 93 108 1.116 . . ID=ACTB1_TAKRU.7;note=*pos 103 ACTB1_TAKRU antigenic epitope 295 301 1.113 . . ID=ACTB1_TAKRU.8;note=*pos 296 ACTB1_TAKRU antigenic epitope 256 266 1.11 . . ID=ACTB1_TAKRU.9;note=*pos 264 ACTB1_TAKRU antigenic epitope 336 352 1.107 . . ID=ACTB1_TAKRU.10;note=*pos 347 ACTB1_TAKRU antigenic epitope 62 76 1.102 . . ID=ACTB1_TAKRU.11;note=*pos 68 ACTB1_TAKRU antigenic epitope 232 250 1.086 . . ID=ACTB1_TAKRU.12;note=*pos 245 ACTB1_TAKRU antigenic epitope 327 332 1.083 . . ID=ACTB1_TAKRU.13;note=*pos 330 ACTB1_TAKRU antigenic epitope 317 323 1.074 . . ID=ACTB1_TAKRU.14;note=*pos 320 ACTB1_TAKRU antigenic epitope 186 192 1.068 . . ID=ACTB1_TAKRU.15;note=*pos 191 ACTB1_TAKRU antigenic epitope 40 46 1.066 . . ID=ACTB1_TAKRU.16;note=*pos 43 ACTB1_TAKRU antigenic epitope 269 275 1.045 . . ID=ACTB1_TAKRU.17;note=*pos 269 ACTB1_TAKRU antigenic epitope 51 57 1.034 . . ID=ACTB1_TAKRU.18;note=*pos 52 Database entry: tsw:actb1_takru ID ACTB1_TAKRU Reviewed; 375 AA. AC P68142; P53484; DT 25-OCT-2004, integrated into UniProtKB/Swiss-Prot. DT 25-OCT-2004, sequence version 1. DT 16-MAY-2012, entry version 49. DE RecName: Full=Actin, cytoplasmic 1; DE AltName: Full=Beta-actin A; DE Contains: DE RecName: Full=Actin, cytoplasmic 1, N-terminally processed; GN Name=actba; OS Takifugu rubripes (Japanese pufferfish) (Fugu rubripes). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; OC Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes; OC Tetradontoidea; Tetraodontidae; Takifugu. OX NCBI_TaxID=31033; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND TISSUE SPECIFICITY. RX MEDLINE=96275651; PubMed=8683572; DOI=10.1006/jmbi.1996.0347; RA Venkatesh B., Tay B.H., Elgar G., Brenner S.; RT "Isolation, characterization and evolution of nine pufferfish (Fugu RT rubripes) actin genes."; RL J. Mol. Biol. 259:655-665(1996). CC -!- FUNCTION: Actins are highly conserved proteins that are involved CC in various types of cell motility and are ubiquitously expressed CC in all eukaryotic cells. CC -!- SUBUNIT: Polymerization of globular actin (G-actin) leads to a CC structural filament (F-actin) in the form of a two-stranded helix. CC Each actin can bind to 4 others. CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton. CC -!- TISSUE SPECIFICITY: Widely distributed. Not expressed in skeletal CC muscle. CC -!- PTM: Oxidation of Met-44 by MICALs (MICAL1, MICAL2 or MICAL3) to CC form methionine sulfoxide promotes actin filament CC depolymerization. Methionine sulfoxide is produced CC stereospecifically, but it is not known whether the (S)-S-oxide or CC the (R)-S-oxide is produced (By similarity). CC -!- MISCELLANEOUS: In vertebrates 3 main groups of actin isoforms, CC alpha, beta and gamma have been identified. The alpha actins are CC found in muscle tissues and are a major constituent of the CC contractile apparatus. The beta and gamma actins coexist in most CC cell types as components of the cytoskeleton and as mediators of CC internal cell motility. CC -!- MISCELLANEOUS: There are three different beta-cytoplasmic actins CC in Fugu rubripes. CC -!- SIMILARITY: Belongs to the actin family. CC ----------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution-NoDerivs License CC ----------------------------------------------------------------------- DR EMBL; U37499; AAC59889.1; -; Genomic_DNA. DR PIR; S71124; S71124. DR ProteinModelPortal; P68142; -. DR SMR; P68142; 2-375. DR Ensembl; ENSTRUT00000013141; ENSTRUP00000013080; ENSTRUG00000005447. DR eggNOG; COG5277; -. DR GeneTree; ENSGT00630000089629; -. DR InParanoid; P68142; -. DR OMA; IKNLMER; -. DR OrthoDB; EOG41JZC9; -. DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-KW. DR GO; GO:0005856; C:cytoskeleton; IEA:UniProtKB-SubCell. DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW. DR InterPro; IPR004000; Actin-like. DR InterPro; IPR020902; Actin/actin-like_CS. DR InterPro; IPR004001; Actin_CS. DR PANTHER; PTHR11937; Actin_like; 1. DR Pfam; PF00022; Actin; 1. DR PRINTS; PR00190; ACTIN. DR SMART; SM00268; ACTIN; 1. DR PROSITE; PS00406; ACTINS_1; 1. DR PROSITE; PS00432; ACTINS_2; 1. DR PROSITE; PS01132; ACTINS_ACT_LIKE; 1. PE 2: Evidence at transcript level; KW Acetylation; ATP-binding; Complete proteome; Cytoplasm; Cytoskeleton; KW Methylation; Nucleotide-binding; Oxidation; Reference proteome. FT CHAIN 1 375 Actin, cytoplasmic 1. FT /FTId=PRO_0000367094. FT INIT_MET 1 1 Removed; alternate (By similarity). FT CHAIN 2 375 Actin, cytoplasmic 1, N-terminally FT processed. FT /FTId=PRO_0000000809. FT MOD_RES 1 1 N-acetylmethionine; in Actin, cytoplasmic FT 1; alternate (By similarity). FT MOD_RES 2 2 N-acetylglutamate; in Actin, cytoplasmic FT 1, N-terminally processed (By FT similarity). FT MOD_RES 44 44 Methionine sulfoxide (By similarity). FT MOD_RES 73 73 Tele-methylhistidine (By similarity). SQ SEQUENCE 375 AA; 41767 MW; 9C505616D33E9495 CRC64; MEDEIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT HTVPIYEGYA LPHAILRLDL AGRDLTDYLM KILTERGYSF TTTAEREIVR DIKEKLCYVA LDFEQEMGTA ASSSSLEKSY ELPDGQVITI GNERFRCPEA LFQPSFLGME SCGIHETTYN SIMKCDVDIR KDLYANTVLS GGTTMYPGIA DRMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWISKQ EYDESGPSIV HRKCF // Output file format The output is a standard EMBOSS feature file. The results can be output in one of several styles by using the command-line qualifier -offormat 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/FeatureFormats.html for further information on feature formats. featmerge writes a single feature table. By default the output is in 'gff' feature format. Output files for usage example File: actb1_takru.gff ##gff-version 3 ##sequence-region ACTB1_TAKRU 1 375 #!Date 2013-07-15 #!Type Protein #!Source-version EMBOSS 6.6.0.0 ACTB1_TAKRU SWISSPROT mature_protein_region 1 375 . . . ID=ACTB1_TAKRU.1;note=Actin%2C cytoplasmic 1;ftid=PRO_0000367094 ACTB1_TAKRU SWISSPROT cleaved_initiator_methionine 1 1 . . . ID=ACTB1_TAKRU.2;note=Removed%3B alternate;comment=By si milarity ACTB1_TAKRU SWISSPROT mature_protein_region 2 375 . . . ID=ACTB1_TAKRU.3;note=Actin%2C cytoplasmic 1%2C N-terminally pro cessed;ftid=PRO_0000000809 ACTB1_TAKRU SWISSPROT post_translationally_modified_region 1 1 . . . ID=ACTB1_TAKRU.4;note=N-acetylmethionine%3B in A ctin%2C cytoplasmic 1%3B alternate;comment=By similarity ACTB1_TAKRU SWISSPROT post_translationally_modified_region 2 2 . . . ID=ACTB1_TAKRU.5;note=N-acetylglutamate%3B in Ac tin%2C cytoplasmic 1%2C N-terminally processed;comment=By similarity ACTB1_TAKRU SWISSPROT post_translationally_modified_region 44 44 . . . ID=ACTB1_TAKRU.6;note=Methionine sulfoxide;comme nt=By similarity ACTB1_TAKRU SWISSPROT post_translationally_modified_region 73 73 . . . ID=ACTB1_TAKRU.7;note=Tele-methylhistidine;comme nt=By similarity ACTB1_TAKRU antigenic epitope 214 222 1.207 . . ID=ACTB1_TAKRU.1;note=*pos 218 ACTB1_TAKRU antigenic epitope 131 145 1.187 . . ID=ACTB1_TAKRU.2;note=*pos 137 ACTB1_TAKRU antigenic epitope 5 12 1.166 . . ID=ACTB1_TAKRU.3;note=*pos 8 ACTB1_TAKRU antigenic epitope 27 38 1.164 . . ID=ACTB1_TAKRU.4;note=*pos 32 ACTB1_TAKRU antigenic epitope 160 183 1.136 . . ID=ACTB1_TAKRU.5;note=*pos 173 ACTB1_TAKRU antigenic epitope 367 372 1.135 . . ID=ACTB1_TAKRU.6;note=*pos 372 ACTB1_TAKRU antigenic epitope 93 108 1.116 . . ID=ACTB1_TAKRU.7;note=*pos 103 ACTB1_TAKRU antigenic epitope 295 301 1.113 . . ID=ACTB1_TAKRU.8;note=*pos 296 ACTB1_TAKRU antigenic epitope 256 266 1.11 . . ID=ACTB1_TAKRU.9;note=*pos 264 ACTB1_TAKRU antigenic epitope 336 352 1.107 . . ID=ACTB1_TAKRU.10;note=*pos 347 ACTB1_TAKRU antigenic epitope 62 76 1.102 . . ID=ACTB1_TAKRU.11;note=*pos 68 ACTB1_TAKRU antigenic epitope 232 250 1.086 . . ID=ACTB1_TAKRU.12;note=*pos 245 ACTB1_TAKRU antigenic epitope 327 332 1.083 . . ID=ACTB1_TAKRU.13;note=*pos 330 ACTB1_TAKRU antigenic epitope 317 323 1.074 . . ID=ACTB1_TAKRU.14;note=*pos 320 ACTB1_TAKRU antigenic epitope 186 192 1.068 . . ID=ACTB1_TAKRU.15;note=*pos 191 ACTB1_TAKRU antigenic epitope 40 46 1.066 . . ID=ACTB1_TAKRU.16;note=*pos 43 ACTB1_TAKRU antigenic epitope 269 275 1.045 . . ID=ACTB1_TAKRU.17;note=*pos 269 ACTB1_TAKRU antigenic epitope 51 57 1.034 . . ID=ACTB1_TAKRU.18;note=*pos 52 Data files None. Notes None. 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 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 pasteseq Insert one sequence into another 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) Peter Rice 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 Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None