aligncopy 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 Reads and writes alignments Description aligncopy reads a set of aligned sequences and reports the alignment using any of the standard EMBOSS alignment formats that can report on the size of the input alignment. An input of two aligned sequences will allow any of the pairwise formats to be used. Other input sizes will reject any pairwise alignment format. Use aligncopypair to print these alignments one pair at a time. Usage Here is a sample session with aligncopy % aligncopy Reads and writes alignments Input (aligned) sequence set: globins.msf Output alignment [globins.aligncopy]: Go to the input files for this example Go to the output files for this example Command line arguments Reads and writes alignments Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequences] seqset File containing a sequence alignment. [-outfile] align [*.aligncopy] Output alignment file name (default -aformat simple) Additional (Optional) qualifiers: -name string Name of the alignment (Any string) -comment string Comment on the alignment (Any string) -append boolean [N] This allows you to append the name and comments you have given on to the end of the existing alignment header. Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequences" 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 "-outfile" associated qualifiers -aformat2 string Alignment format -aextension2 string File name extension -adirectory2 string Output directory -aname2 string Base file name -awidth2 integer Alignment width -aaccshow2 boolean Show accession number in the header -adesshow2 boolean Show description in the header -ausashow2 boolean Show the full USA in the alignment -aglobal2 boolean Show the full sequence in alignment 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 aligncopy reads aligned 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 File: globins.msf !!AA_MULTIPLE_ALIGNMENT 1.0 ../data/globins.msf MSF: 164 Type: P 25/06/01 CompCheck: 4278 .. Name: HBB_HUMAN Len: 164 Check: 6914 Weight: 0.61 Name: HBB_HORSE Len: 164 Check: 6007 Weight: 0.65 Name: HBA_HUMAN Len: 164 Check: 3921 Weight: 0.65 Name: HBA_HORSE Len: 164 Check: 4770 Weight: 0.83 Name: MYG_PHYCA Len: 164 Check: 7930 Weight: 1.00 Name: GLB5_PETMA Len: 164 Check: 1857 Weight: 0.91 Name: LGB2_LUPLU Len: 164 Check: 2879 Weight: 0.43 // 1 50 HBB_HUMAN ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR HBB_HORSE ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR HBA_HUMAN ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS HBA_HORSE ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG MYG_PHYCA ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD 51 100 HBB_HUMAN FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE HBB_HORSE FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE HBA_HUMAN FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD HBA_HORSE FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD MYG_PHYCA KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN 101 150 HBB_HUMAN LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA HBB_HORSE LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA HBA_HUMAN LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS HBA_HORSE LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS MYG_PHYCA SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA 151 164 HBB_HUMAN NALAHKYH~~~~~~ HBB_HORSE NALAHKYH~~~~~~ HBA_HUMAN TVLTSKYR~~~~~~ HBA_HORSE TVLTSKYR~~~~~~ MYG_PHYCA KDIAAKYKELGYQG GLB5_PETMA Y~~~~~~~~~~~~~ LGB2_LUPLU IVIKKEMNDAA~~~ Output file format The output is a standard EMBOSS alignment file. The results can be output in one of several styles by using the command-line qualifier -aformat xxx, where 'xxx' is replaced by the name of the required format. Some of the alignment formats can cope with an unlimited number of sequences, while others are only for pairs of sequences. The available multiple alignment format names are: multiple, simple, fasta, msf, clustal, mega, meganon, nexus,, nexusnon, phylip, phylipnon, selex, treecon, tcoffee, debug, srs. The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, match, sam, bam, score, srspair See: http://emboss.sf.net/docs/themes/AlignFormats.html for further information on alignment formats. Output files for usage example File: globins.aligncopy ######################################## # Program: aligncopy # Rundate: Fri 15 Jul 2011 12:00:00 # Commandline: aligncopy # -sequences ../../data/globins.msf # Align_format: simple # Report_file: globins.aligncopy ######################################## #======================================= # # Aligned_sequences: 7 # 1: HBB_HUMAN # 2: HBB_HORSE # 3: HBA_HUMAN # 4: HBA_HORSE # 5: MYG_PHYCA # 6: GLB5_PETMA # 7: LGB2_LUPLU # Matrix: EBLOSUM62 # # Length: 164 # Identity: 1/164 ( 0.6%) # Similarity: 93/164 (56.7%) # Gaps: 31/164 (18.9%) # # #======================================= HBB_HUMAN 1 --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQR 40 HBB_HORSE 1 --------VQLSGEEKAAVLALWDKVN-EEEVGGEALGR-LLVVYPWTQR 40 HBA_HUMAN 1 --------------VLSPADKTNVKAA-WGKVGAHAGEYGAEALERMFLS 35 HBA_HORSE 1 --------------VLSAADKTNVKAA-WSKVGGHAGEYGAEALERMFLG 35 MYG_PHYCA 1 -------VLSEGEWQLVLHVWAKVEAD-VAGHGQDILIR-LFKSHPETLE 41 GLB5_PETMA 1 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE 50 LGB2_LUPLU 1 --------GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD 42 :: : : :.: : : : :::: :: : : : : HBB_HUMAN 41 FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE 90 HBB_HORSE 41 FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE 90 HBA_HUMAN 36 FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD 85 HBA_HORSE 36 FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD 85 MYG_PHYCA 42 KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ 91 GLB5_PETMA 51 FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD 100 LGB2_LUPLU 43 LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN 92 :: :: :: : : :: ::: :::::: :: : : :::::: : |:: HBB_HUMAN 91 LHCDKLH--VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA 138 HBB_HORSE 91 LHCDKLH--VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA 138 HBA_HUMAN 86 LHAHKLR--VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS 133 HBA_HORSE 86 LHAHKLR--VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS 133 MYG_PHYCA 92 SHATKHK--IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR 139 GLB5_PETMA 101 LSGKHAK--SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA 148 LGB2_LUPLU 93 LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA 142 ::: ::: ::: ::::: : :: ::: : :::::: ::: : :: :: HBB_HUMAN 139 NALAHKYH------ 146 HBB_HORSE 139 NALAHKYH------ 146 HBA_HUMAN 134 TVLTSKYR------ 141 HBA_HORSE 134 TVLTSKYR------ 141 MYG_PHYCA 140 KDIAAKYKELGYQG 153 GLB5_PETMA 149 Y------------- 149 LGB2_LUPLU 143 IVIKKEMNDAA--- 153 : :: #--------------------------------------- #--------------------------------------- Data files For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAFULL is used. EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA. To see the available EMBOSS data files, run: % embossdata -showall To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run: % embossdata -fetch -file Exxx.dat Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata". The directories are searched in the following order: * . (your current directory) * .embossdata (under your current directory) * ~/ (your home directory) * ~/.embossdata 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 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 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) Jon Ison 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