Warning: this documents contains the original documentation of the program consensus, developed by Jerry Hertz. Options are indicated as they are used in the unix shell.

The web interface presents the same options with a different user interface.

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Copyright 1990--1998 Gerald Z. Hertz
May be copied for noncommercial purposes.

Author:
  Gerald Z. Hertz
  Dept. of Molecular, Cellular, and Developmental Biology
  University of Colorado
  Campus Box 347
  Boulder, CO  80309-0347

  hertz@colorado.edu



CONSENSUS (version 6a)

This program determines consensus patterns in unaligned sequences.  The
algorithm is based on a matrix representation of a consensus pattern.  Each
row corresponds to one of the letters of the relevant alphabet---e.g., 4
rows in the case of DNA.  Each column corresponds to one of the positions
within the pattern.  The elements of the matrix are determined by the
number of times that the indicated letter occurs at the indicated position.

Matrices are constructed by sequentially adding additional L-mers
(subsequences of length L, where L is the width of the pattern being
sought) to previously saved matrices.  During each cycle, only the
most significant matrices are saved.  The maximum number of matrices to
save is determined by the "-q" option (see section 1 below).  In
practice, less matrices are ultimately saved because many of the
matrices initially saved are identical to each other.

The program can use 3 different criteria for deciding to stop adding
additional words to the saved matrices:
1) Each sequence has contributed exactly one word to the saved
   matrices (the default).
2) The saved matrices contain a maximum allowable number of words (set
   with the -n and -N options).
3) The program has completed a designated number of cycles since finding
   the current most significant alignment (set with the -t option).
   This latter criteria is used in addition to criteria 1 and 2
   to terminate the program sooner.

The significance of a matrix is initially measured by its information
content.  A higher information content indicates a rarer pattern and a
more desirable matrix.  The program also estimates for each matrix a
p-value, which is the probability of observing the particular
information content or higher in an arbitrary alignment of random
L-mers.  The ultimate statistical significance of a matrix is
determined by multiplying the p-value by the approximate number of
possible alignments, containing the designated number of sequences and
having the observed width.  We refer to this product as the expected
frequency of the matrix alignment.  The expected frequency allows the
comparison of matrices summarizing differing numbers of sequences and
having differing widths.

The program can print two different lists of matrices.  The first list
contains the matrices having the highest information content from each
cycle, ordered by decreasing statistical significance (i.e.,
increasing expected frequency).  In general, this first list will
contain the most interesting alignment.  The second list contains the
matrices saved after the final cycle of the program, also ordered by
decreasing statistical significance.  In general, this latter list
will be useful when the user wishes each sequence to contribute
exactly one word to the final alignment (i.e., when the -n and -N
options are not used).

In the program's output, the words contained in each matrix are listed
in the order of their occurrence in the input sequences.  The order is
indicated by "integer|integer".  The first integer is simply a
sequential count of the words, and the second integer indicates during
which cycle the word was added to the matrix.  The location of a word
is indicated by "integer/integer".  The first integer indicates which
sequence contains the word, and the second integer indicates where in
that sequence the word is located.  If the first integer is preceded
by a minus sign, then the complementary word is the one included in
the matrix.

The output of the program is sent to the standard output.  The input
files---those containing the actual sequences and those indicated by
the "-f", "-a", and "-i" options---can contain comments according to
the following convention.  The portion of a line following a ';', '%',
or '#' is considered a comment and is ignored.  Comments can begin
anywhere in a line and always end at the end of the line.  The one
minor exception is that, to avoid ambiguity, comments in the list of
sequences (see the "-f" option below) must be preceded by a blank
space when not occurring at the beginning of a line.


COMMAND LINE OPTIONS:

 0) -h: print these directions.

 1) General information
    -f filename: this file (default: read from the standard input) contains
       the names of the sequences.  The names of the sequences must be
       less than 512 characters.  The corresponding sequence may follow
       its name if the sequence is enclosed between backslashes (\).
       Otherwise, the sequence is assumed to be in a separate file having
       the indicated name.  The format of the actual sequences is described
       at the end of these directions.  The following four modifiers can
       appear in front of the name of the relevant sequence:
       -c: the sequence is circular.
       -s integer-integer integer-integer: the positions in the sequence
          indicated by the integer pairs, inclusive, are seed sequences.
          If the "-s" modifier is used anywhere in the input file, then the
          initial set of matrices will only be constructed (i.e., seeded)
          from the sequences within the marked regions.  If this modifier
          is not used anywhere in the input file, then all the sequences
          will be used to seed matrices.  One or more integer pair can be
          indicated for a single sequence.  However, if no integer pairs
          are given, the whole sequence will be used for seeding matrices.
       -i integer-integer integer-integer: the positions in the sequence
          indicated by the integer pairs, inclusive, are the only positions
          to be analyzed.
       -e integer-integer integer-integer: the positions in the sequence
          indicated by the integer pairs, inclusive, are to be excluded
          from the analysis.
       When both the "-i" and "-e" modifiers are used, the intersection
       of permissible positions is analyzed.  When a sequence name is
       not marked by either the "-i" or "-e" modifier, then the whole
       sequence is included in the analysis.

    -L integer: width of the pattern being sought (required).

    -q integer: the maximum number of matrices to save between cycles of the
       program---i.e., the queue size (default: save 1000 matrices).

 2) Alphabet options

    -d: use the designated prior probabilities of the letters to override the
        observed frequencies.  By default, the program uses the frequencies
        observed in your own sequence data for the prior probabilities of the
        letters.  However, if the "-d" option is set, the prior probabilities
        designated by one of the next 3 options are used.  If the "-d" option
        is not set, the next 3 options are still used to determine the
        sequence alphabet, but any prior probability information is ignored.

    The next three options are mutually exclusive (default: "-a alphabet").
    -a filename: file containing the alphabet and normalization information.
       [Use "-af" when using the VMS operating system]

       Each line contains a letter (a symbol in the alphabet) followed by an
       optional normalization number (default: 1.0).  The normalization is
       based on the relative prior probabilities of the letters.  For nucleic
       acids, this might be be the genomic frequency of the bases; however,
       if the "-d" option is not used, the frequencies observed in your own
       sequence data are used.  In nucleic acid alphabets, a letter and its
       complement appear on the same line, separated by a colon (a letter can
       be its own complement, e.g. when using a dimer alphabet).
       Complementary letters may use the same normalization number.  Only the
       standard 26 letters are permissible; however, when the "-CS" option is
       used, the alphabet is case sensitive so that a total of 52 different
       characters are possible.

       POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS:
       letter
       letter normalization

       POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS:
       letter:complement
       letter:complement normalization
       letter:complement normalization:complement's_normalization

    -i filename: same as the "-a" option, except that the symbols of
       the alphabet are represented by integers rather than by letters.
       Any integer permitted by the machine is a permissible symbol.
       [Use "-if" when using the VMS operating system]

    -A alphabet_and_normalization_information: same as "-a" option, except
       information appears on the command line (e.g., -A a:t 3 c:g 2).
       [Use "-ac" when using the VMS operating system]

 3) Alphabet modifier indicating whether ascii alphabets are case
    sensitive---the following option is mutually exclusive with
    the "-i" option (default: ascii alphabets are case insensitive).
    -CS: ascii alphabets are case sensitive.
         [Use "-as" when using the VMS operating system]

 4) Options for handling the complement of nucleic acid sequences---
    the four options in this section are mutually exclusive
    -c0: ignore the complement (the default option)
    -c1: include both strands as separate sequences
    -c2: include both strands as a single sequence (i.e., orientation unknown)
    -c3: assume pattern is symmetrical

 5) Algorithm options
       the "-pr1" and "-pr2" options are mutually exclusive;
       the "-l", "-n", and "-N" options are mutually exclusive;
       the "-m" option can only be used when the "-n" or "-N" option is used.

    -pr1: save the top progeny matrices regardless of parentage.
    -pr2: try to save the top progeny matrices for each parental matrix (the
       default).  This option prevents a strong pattern found in only a subset
       of the sequences from overwhelming the algorithm and eliminating other
       potential patterns.  This undesirable situation can occur when a
       subset of the sequences share an evolutionary relationship not
       common to the majority of the sequences.  This option corresponds
       to the original "consensus" algorithm (Stormo and Hartzell, 1989,
       PNAS, 86:1183-1187; Hertz et al., 1990, CABIOS, 6:81-92).

    -l: (lowercase L) seed with the first sequence and proceed linearly
       through the list.  This option results in a significant speed
       up in the program, but the algorithm becomes dependent on the
       order of the sequence-file names.  This option corresponds to
       the original "consensus" algorithm (Stormo and Hartzell, 1989,
       PNAS, 86:1183-1187; Hertz et al., 1990, CABIOS, 6:81-92).

    -n integer: repeat the matrix building cycle a maximum of "integer"
       times and allow each sequence to contribute zero or more words
       per matrix.  [Use "-n1" when using the VMS operating system]
    -N integer: repeat the matrix building cycle a maximum of "integer"
       times and allow each sequence to contribute one or more words
       per matrix.  [Use "-n2" when using the VMS operating system]

    -m integer: the minimum distance between the starting points of words
       within the same matrix pattern; must be a positive integer; can only
       be used when the "-n" or "-N" option is also used.  If the integer
       is a 1, then there is no restriction on the overlap.  If the integer
       is the same as the integer indicated by the "-L" option, then no
       overlap is allowed (default: integer indicated by the "-L" option).
       When the "-c2" option is used (see below), then the "-m" option also
       indicates the minimum distance between the start of a word and the
       end of a word on the complementary strand.

    -t integer: terminate the program "integer" cycles after the current
       most significant alignment is identified (default: terminate only
       when the maximum number of matrix building cycles is completed).

    The "-q", "-n", and "-t" options can be changed after the program
    starts by placing the new options in a file called "changes." suffixed
    with the process identification number---the PID number listed at the
    beginning of the program's output.  For example a file called
    "changes.10568" might contain "-q10 -n50 -t2".  The "-n" option
    can change the maximum number of words in the alignments even if it
    was not used at the beginning of the program, although it will not
    permit a sequence to contribute more than one word to the alignment
    unless the "-n" or "-N" option was used on the command line.  If
    the "-t" option was not used when the program was started, this option
    will only keep track of alignments beginning with the cycle during
    which it is first initiated.

 6) Output options
    -pt integer: the number of matrices to print of the top matrices from each
       cycle (default: 4).  A negative value means print all the top matrices.
    -pf integer: the number of matrices to print of the matrices saved from
       the final cycle (default when NOT using "-n" or "-N" options: print 4
       matrices; default when using "-n" option: print no matrices).



FORMAT OF THE SEQUENCE FILES

Do not explicitly give the complements of nucleic acid sequences.  If
needed, the complementary sequence is determined by the program.
Whitespace, periods, dashes (unless part of an integer when the "-i"
option is used), and comments beginning with ';', '%', or '#' are
ignored.  When using letter characters (i.e., with the "-a" and "-A"
alphabet options), integers are also ignored so that the sequence file
can contain positional information.  When using integer characters
(i.e., with the "-i" alphabet option) the integers must be separated
by whitespace.

Sequences surrounded by slashes (/) do not contribute to the
generation of the patterns; thus, a portion of a sequence can be
ignored without disrupting the overall numbering of the sequence.
A double slash (//) would indicate a discontinuity in the sequence.
A '/' at the beginning or the end of a sequence will cause the sequence
to be marked as non-circular even if the sequence's name is marked
with a "-c" (see the "-f" option in section 1).  The effect of the
single slashes can also be created with the "-i" and "-e" modifiers in
the file containing the names of the sequences (see the "-f" option in
section 1).  When slashes and the "-i" and "-e" modifiers are all
used, the intersection of permissible positions is analyzed.

Sequences that follow their name in the file indicated by the "-f"
option must be enclosed between backslashes (\) (i.e., the actual
sequence must be preceded and followed by a backslash).  However, if
the sequence is contained in a separate file, do NOT use a '\'.