Methods for calculating the probabilities of finding patterns in sequences.

by: R Staden

Comput Appl Biosci, Vol. 5, No. 2. (April 1989), pp. 89-96.

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Abstract

This paper describes the use of probability-generating functions for calculating the probabilities of finding motifs in nucleic acid and protein sequences. Equations and algorithms are given for calculating the probabilities associated with nine different ways of defining motifs. Comparisons are made with searches of random sequences. A higher level structure--the pattern--is defined as a list of motifs. A pattern also specifies the permitted ranges of spacing allowed between its constituent motifs. Equations for calculating the expected numbers of matches to patterns are given.

@article{citeulike:2552400, abstract = {This paper describes the use of probability-generating functions for calculating the probabilities of finding motifs in nucleic acid and protein sequences. Equations and algorithms are given for calculating the probabilities associated with nine different ways of defining motifs. Comparisons are made with searches of random sequences. A higher level structure--the pattern--is defined as a list of motifs. A pattern also specifies the permitted ranges of spacing allowed between its constituent motifs. Equations for calculating the expected numbers of matches to patterns are given.}, address = {MRC Laboratory of Molecular Biology, Cambridge, UK.}, author = {Staden, R. }, citeulike-article-id = {2552400}, issn = {0266-7061}, journal = {Comput Appl Biosci}, keywords = {cis\_regulatory\_elements, motif\_searching}, month = {April}, number = {2}, pages = {89--96}, posted-at = {2008-03-18 18:10:27}, priority = {2}, title = {Methods for calculating the probabilities of finding patterns in sequences.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/2720468}, volume = {5}, year = {1989} }

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TY - JOUR ID - citeulike:2552400 TI - Methods for calculating the probabilities of finding patterns in sequences. JF - Comput Appl Biosci VL - 5 IS - 2 SP - 89 EP - 96 AD - MRC Laboratory of Molecular Biology, Cambridge, UK. SN - 0266-7061 N2 - This paper describes the use of probability-generating functions for calculating the probabilities of finding motifs in nucleic acid and protein sequences. Equations and algorithms are given for calculating the probabilities associated with nine different ways of defining motifs. Comparisons are made with searches of random sequences. A higher level structure--the pattern--is defined as a list of motifs. A pattern also specifies the permitted ranges of spacing allowed between its constituent motifs. Equations for calculating the expected numbers of matches to patterns are given. KW - cis_regulatory_elements KW - motif_searching AU - Staden, R PY - 1989/04// UR - http://view.ncbi.nlm.nih.gov/pubmed/2720468 ER -

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