                                   eomega



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Function

   Multiple sequence alignment (ClustalO wrapper)

Description

   eomega is a wrapper to clustalo. It takes a set of unaligned sequences
   and produces an output alignment.

   Clustal-Omega (clustalo) is a general purpose multiple sequence
   alignment (MSA) program for proteins. It produces high quality MSAs and
   is capable of handling data-sets of hundreds of thousands of sequences
   in reasonable time.

   In its current form Clustal-Omega can only align protein sequences but
   not DNA/RNA sequences. It is envisioned that DNA/RNA will become
   available in a future version.

Algorithm

   Clustal-Omega uses HMMs for the alignment engine, based on the HHalign
   package from Johannes Soeding [1]. Guide trees are optionally made
   using mBed [2] which can cluster very large numbers of sequences in
   O(N*log(N)) time. Multiple alignment then proceeds by aligning larger
   and larger alignments using HHalign, following the clustering given by
   the guide tree.

Usage

   Here is a sample session with eomega


% eomega globins.fasta
Multiple sequence alignment (ClustalO wrapper)
(aligned) output sequence set [globins.aln]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Multiple sequence alignment (ClustalO wrapper)
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     File containing sequences to align
  [-outseq]            seqoutset  [.] Sequence set filename
                                  and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -indistfile         infile     Pairwise distance matrix input file (skips
                                  distance computation)
   -inguidefile        infile     Guide tree input file (skips distance
                                  computation and guide tree clustering step)
   -dealign            toggle     [N] Dealign input sequences
   -cluster            menu       [mbed] Method (Values: mbed (mBED method);
                                  full (Full slow method); iter (Iteration
                                  used full slower method))
   -maxiterations      integer    [0] Number of (combined guide tree/HMM)
                                  iterations (Integer from 0 to 2000000000)
   -maxgiterations     integer    [2000000000] Maximum guide tree iterations
                                  (Integer from 0 to 2000000000)
   -maxhiterations     integer    [2000000000] Maximum number of HMM
                                  iterations (Integer from 0 to 2000000000)
   -maxseqs            integer    [2000000000] Maximum number of sequences
                                  (Integer from 2 to 2000000000)
   -maxlenseq          integer    [2000000000] Maximum length of sequence
                                  (Integer from 1 to 2000000000)
   -self               toggle     [N] Set options automatically (might
                                  overwrite some options
   -outformat          menu       [fasta] Format (Values: fasta (FASTA);
                                  clustal (Aln clustal); msf (MSF); phylip
                                  (Phylip); selex (Selex); stockholm
                                  (Stockholm); vienna (ViennaRNA))
   -outdistfile        outfile    [*.eomega] Pairwise distance matrix output
                                  file, only available in cluster mode 'full'
   -outguidefile       outfile    [*.eomega] Guide tree output file
   -log                toggle     [N] Log progress to standard output if not
                                  used for output

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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

   "-outdistfile" associated qualifiers
   -odirectory         string     Output directory

   "-outguidefile" associated qualifiers
   -odirectory         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

   eomega reads a set of unaligned sequences and optional distance and
   guide tree files.

  Input files for usage example

  File: globins.fasta

>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
EFTPPVQAAYQKVVAGVANALAHKYH
>HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
DFTPELQASYQKVVAGVANALAHKYH
>HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR
>HBA_HORSE Sw:Hba_Horse => HBA_HORSE
VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
VHASLDKFLSSVSTVLTSKYR
>MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
AVIADTVAAGDAGFEKLMSMICILLRSAY
>LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA

Output file format

   eomega writes alignments using the default Clustal-Omega output.

  Output files for usage example

  File: globins.aln

>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
--------VHLTPEEKSAVTALWGKVNV--DEVGGEALGRLLVVYPWTQRFFESFGDLST
PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLK--G---TFATLSELHCDKLHVDPENFRL
LGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------
>HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
--------VQLSGEEKAAVLALWDKVNE--EEVGGEALGRLLVVYPWTQRFFDSFGDLSN
PGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLK--G---TFAALSELHCDKLHVDPENFRL
LGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH------
>HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
---------VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDL---
---SHGSAQVKGHGKKVADALTNAVAHVDDMP--N---ALSALSDLHAHKLRVDPVNFKL
LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------
>HBA_HORSE Sw:Hba_Horse => HBA_HORSE
---------VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDL---
---SHGSAQVKAHGKKVGDALTLAVGHLDDLP--G---ALSNLSDLHAHKLRVDPVNFKL
LSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR------
>MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
---------VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKT
EAEMKASEDLKKHGVTVLTALGAILKKKGHHE--A---ELKPLAQSHATKHKIPIKYLEF
ISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTE--KMSMKLRDLSGKHAKSFQVDPQYFKV
LAAVIADTVAA---------GDAGFEKLMSMICILLRSAY-------
>LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
--------GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSE
--VPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGV-ADAHFPV
VKEAILKTIKEVVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA---

Data files

   None.

Notes

   In the clustal-omega README file, this is input option (a).

References

   [1] Johannes Soding (2005) Protein homology detection by HMM-HMM
   comparison. Bioinformatics 21 (7): 951aEUR"960.

   [2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence
   embedding for fast construction of guide trees for multiple sequence
   alignment. Algorithms Mol Biol. 2010 May 14;5:21.

   [3] http://www.genetics.wustl.edu/eddy/software/#squid

   [4] Wilbur and Lipman, 1983; PMID 6572363

   [5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving
   the sensitivity of progressive multiple sequence alignment through
   sequence weighting, position-specific gap penalties and weight matrix
   choice. Nucleic Acids Res., 22, 4673-4680.

   [6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA,
   McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD,
   Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0.
   Bioinformatics, 23, 2947-2948.

   [7] Kimura M (1980). "A simple method for estimating evolutionary rates
   of base substitutions through comparative studies of nucleotide
   sequences". Journal of Molecular Evolution 16: 111aEUR"120.

   [8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
   accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   edialign         Local multiple alignment of sequences
   emma             Multiple sequence alignment (ClustalW wrapper)
   eomegapp         Profile with profile (ClustalO wrapper)
   eomegaps         Single sequence with profile (ClustalO wrapper)
   eomegash         Sequence with HMM (ClustalO wrapper)
   eomegasp         Sequence with profile (ClustalO wrapper)
   infoalign        Display basic information about a multiple sequence alignment
   mse              Multiple sequence editor
   plotcon          Plot conservation of a sequence alignment
   prettyplot       Draw a sequence alignment with pretty formatting
   showalign        Display a multiple sequence alignment in pretty format
   tranalign        Generate an alignment of nucleic coding regions from aligned
                    proteins

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

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
