What is SeLOX useful for ?

SeLOX identifies lox-like sites in genomic sequences. Recombinases are used as functional genomic tools to remove genomic regions lying between lox-like sites. These sites are characterized by two reverse complement stretches of 13 bp length separated by a spacer.

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How does SeLOX work ?

SeLOX works by transforming both the position weight matrix formed from the query lox-like sites and the sequences to be searched into bit strings, and subsequently performing a binary AND operation

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What is the format of the output ?

SeLOX groups the sequences in which a match has been found by the lox-like site present in that sequence. This gives an idea of what site is present across as many input sequences as possible. SeLOX marks the nucleotides which are either mismatches to the position weight matrix used as the query or those nucleotides which are not reverse complements in the corresponding positions. The mismatches are marked by dots on top of the nucleotide, and the asymmetry by dots below the nucleotide.

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How is the score calculated ?

A naive scoring of each result is done using the weights from the position weight matrix used as query. A match at a position results in a positive score equal to the weight for the nucleotide matched at that position, and a mismatch at a position yields a negative score of the maximum weight derived for that particular position. We sum up all the scores at all the positions to comput the final score