
                                   cons 



Function

   Create a consensus sequence from a multiple alignment

Description

   cons calculates a consensus sequence from a multiple sequence
   alignment. To obtain the consensus, the sequence weights and a scoring
   matrix are used to calculate a score for each amino acid residue or
   nucleotide at each position in the alignment. The highest scoring
   residue goes into the consensus sequence if the score is higher than a
   user-specified "plurality" value, otherwise, there is no consensus at
   that position.

Algorithm

   To obtain the consensus, the sequence weights and a scoring matrix are
   used to calculate a score at each position in the alignment as
   follows. The residue (or nucleotide) i in an alignment column, is
   compared to all other residues (j) in the same column. The score for i
   is the sum over all residues j (not i=j) of the score(ij)*weight(j),
   where score(ij) is taken from a nucleotide or protein scoring matrix
   (see -datafile qualifier) and the "weight(j)" is the weighting given
   to the sequence j, which is given in the alignment file.

   The highest scoring type of residue is then found in the column. If
   the number of "positive matches" (see below) for this residue is
   greater than the "plurality value" (see below), then this residue is
   the consensus residue. Otherwise there is no consensus for that
   position and an 'n' (nucleotide sequence alignment) or an 'x' (protein
   sequence alignment) character is written to the consensus sequence.

   The positive matches for a residue i are calculated as being the sum
   of the corresponding sequence weights for all the residues that
   increase the score of residue i (i.e. that have a positive score). The
   "plurality" qualifier sets the cut-off for the number of positive
   matches (weighted) below which there is no consensus.

Usage

   Here is a sample session with cons


% cons 
Create a consensus sequence from a multiple alignment
Input (aligned) sequence set: dna.msf
output sequence [dna.fasta]: aligned.cons

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     File containing a sequence alignment.
  [-outseq]            seqout     [.] Sequence filename and
                                  optional format (output USA)

   Additional (Optional) qualifiers:
   -datafile           matrix     [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.
   -plurality          float      [Half the total sequence weighting] Set a
                                  cut-off for the number of positive matches
                                  below which there is no consensus. The
                                  default plurality is taken as half the total
                                  weight of all the sequences in the
                                  alignment. (Any numeric value)
   -identity           integer    [0] Provides the facility of setting the
                                  required number of identities at a site for
                                  it to give a consensus at that position.
                                  Therefore, if this is set to the number of
                                  sequences in the alignment only columns of
                                  identities contribute to the consensus.
                                  (Integer 0 or more)
   -setcase            float      [@( $(sequence.totweight) / 2)] Sets the
                                  threshold for the positive matches above
                                  which the consensus is is upper-case and
                                  below which the consensus is in lower-case.
                                  (Any numeric value)
   -name               string     Name of the consensus sequence (Any string
                                  is accepted)

   Advanced (Unprompted) qualifiers: (none)
   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. 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

Input file format

   The USA of a set of aligned sequences.

  Input files for usage example

  File: dna.msf

!!NA_MULTIPLE_ALIGNMENT

 dna.msf  MSF: 120  Type: N  January 01, 1776  12:00  Check: 3196 ..

 Name: MSFM1          Len:   120  Check:  8587  Weight:  1.00
 Name: MSFM2          Len:   120  Check:  6178  Weight:  1.00
 Name: MSFM3          Len:   120  Check:  8431  Weight:  1.00

//

        MSFM1  ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC
        MSFM2  ACGTACGTAC GTACGTACGT ....ACGTAC GTACGTACGT ACGTACGTAC
        MSFM3  ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT CGTACGTACG

        MSFM1  GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT
        MSFM2  GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT
        MSFM3  TACGTACGTA CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT

        MSFM1  ACGTACGTAC GTACGTACGT
        MSFM2  ACGTACGTTG CAACGTACGT
        MSFM3  ACGTACGTAC GTACGTACGT

Output file format

   The output consists of a sequence file holding the consensus sequence.

  Output files for usage example

  File: aligned.cons

>EMBOSS_001
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT

Data files

   cons uses the standard set of scoring matrix data files in the EMBOSS
   data directory.

   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

   The "identity" qualifier provides an additional constrain to
   "plurality" when determining a consensus residue at an alignment site.
   "identity" sets the required number of identities at a site for it to
   be included in the consensus. If for example this is set to the number
   of sequences in the alignment, then only a site with the same residue
   in all sequences would be included in the consensus.

   The "setcase" qualifier sets the threshold for the positive matches
   above which the consensus residue is given is upper-case and below
   which it is in lower-case.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name Description
   consambig Create an ambiguous consensus sequence from a multiple
   alignment
   megamerger Merge two large overlapping DNA sequences
   merger Merge two overlapping sequences

Author(s)

   Tim Carver (tcarver © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Target users

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

Comments

   None
