are studying rather than assuming equal probabilities of each letter (e.g., the GC-content of DNA of thermophilic bacteria range from 65.3 to 70.8, thus a motif of ATAT would contain much more information than a motif of CCGG). The equation for information content thus becomes where is the background frequency for letter . This corresponds to the Kullback–Leibler divergence or relative entropy. However, it has been shown that when using PSSM to search genomic sequences (see below) this uniform correction can lead to overestimation of the importance of the different bases in a motif, due to the uneven distribution of n-mers in real genomes, leading to a significantly larger number of false positives. Uses There are various algorithms to scan for hits of PWMs in sequences. One example is the MATCH algorithm which has been implemented in the ModuleMaster. More sophisticated algorithms for fast database searching with nucleotide as well as amino acid PWMs/PSSMs are implemented in the possumsearch software. See also ScerTF References External links 3PFDB – a database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach. UGENE – PSS matrices design, integrated interface to JASPAR, UniPROBE and SITECON databases. Bioinformatics Evaluation methods