|
Consensus (version 6c) |
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.
* POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS:
* POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS:
Input sequence can be either of FASTA format or Consensus Format. If FASTA format sequences are given, the program will convert them to Consensus format internally before running the Consensus or Patser program.
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 '\'.