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DESCRIPTION

This module computes the e-value and h-value as the number of expected and observed hits for a given word length.
However, the actual number of words in the genome being searched for is usually different to the genome being searched. For example, if you have a protein search, you want the protein itself, as well as those parts of the genome that align to it. These are often called «quasi-exact» matches. You can tell FASTA which number of words to search for by using the parameter «-o».
The default is to search for all words of length 3 and up, which will be known as «exact matches». To search for words of length 3 and up which are «quasi-exact matches», use «-o length».
This option works by computing the e-value and h-value as the number of expected and observed hits for a given word length. The h-value is then divided by the total number of possible words.
KEYENUM Description:

DESCRIPTION

Lets you define the numbers of words to search for.

NUM_WORDS

This parameter defaults to 1. It can be set to more or less than 1 to allow the ktup parameter to be adjusted in order to search for a set number of words.

NUM_WORD_HITS

This parameter defaults to 0. It can be set to more or less than 0 to allow the ktup parameter to be adjusted in order to search for a set number of words.

ONLY_WORDS

This parameter defaults to FALSE. If TRUE, then only exact word matches are reported. If FALSE, then exact, quasi-exact and non-exact matches are reported.

NUMBER_OF_HIT_RECORDS

This parameter defaults to 0. It can be set to more or less than 0 to change the number of record (locus) entries that are output to the result-file. The actual number of words that are searched for is given by the ktup parameter.

LIST_ONLY

This parameter defaults to FALSE. If TRUE, then the results are output only. Otherwise, they are output in the format of a FASTA file.

MAP_ONLY

This parameter defaults to FALSE. If TRUE, then a one-to-one mapping is output to a text file. 384a16bd22

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