dipwmsearch
Protein binding sites in DNA or RNA sequences are modeled by probabilistic motifs. A Position Weight Matrix (PWM) is a simple, powerful, and widely used representation of such motifs. Because PWMs assume that sequence positions are independent of eachother (which is too restrictive for some binding or interaction sites), a generalisation of PWMs, termed di-nucleotidic PWMs (di-PWMs) have been introduced by Kulakovskiy et al. 2013 Kulakovskiy_2013. For instance, the HOCOMOCO database is a collection of PWMs and di-PWMs for Transcription Factor binding sites Kulakovskiy_2018.
This package, called dipwmsearch, offers you efficient algorithms to search for occurrences of di-PWMs motifs in DNA or RNA sequences. The search sequence may contain positions with non-ATGC symbols, encoded with IUPAC. A description of the algorithms implemented in this package is available in our article dipwmsearch_2022.
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