Article

Combining evidence using P‐values: application to sequence homology searches

San Diego Supercomputer Center, CA 92186-9784, USA.
Bioinformatics (Impact Factor: 4.98). 02/1998; 14(1):48-54. DOI: 10.1093/bioinformatics/14.1.48
Source: PubMed

ABSTRACT

MOTIVATION: To illustrate an intuitive and statistically valid method for combining independent sources of evidence that yields
a p-value for the complete evidence, and to apply it to the problem of detecting simultaneous matches to multiple patterns
in sequence homology searches. RESULTS: In sequence analysis, two or more (approximately) independent measures of the membership
of a sequence (or sequence region) in some class are often available. We would like to estimate the likelihood of the sequence
being a member of the class in view of all the available evidence. An example is estimating the significance of the observed
match of a macromolecular sequence (DNA or protein) to a set of patterns (motifs) that characterize a biological sequence
family. An intuitive way to do this is to express each piece of evidence as a p-value, and then use the product of these p-values
as the measure of membership in the family. We derive a formula and algorithm (QFAST) for calculating the statistical distribution
of the product of n independent p-values. We demonstrate that sorting sequences by this p-value effectively combines the information
present in multiple motifs, leading to highly accurate and sensitive sequence homology searches.

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    • "(7) Each time a motif is matched to a position in the protein sequence, a p-value is calculated that represents the probability of finding a match as good as the observed match within a random sequence. The p-values for all motifs in a single sequence are then combined using QFAST to obtain the final statistical significance score (final p-value) (Bailey and Gribskov, 1998a). (8) The protein information (including accession numbers, annotations, and species), final p-value, and sequence fragments matched to each queried motif are exported for all sequences with a final p-value more significant than a user-selected p-value. "
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    • ". Variable width motifs for non-regulated, destabilized and stabilized genes. 3'-UTR analysis was using the MEME software analysis package [1] [2] with parameters adjusted for variable-width motifs (7 – 15 nt) on non-regulated, destabilized, and stabilized transcripts. Significant motifs from MEME analysis are shown for destabilized, stabilized, and non-regulated datasets. "

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    • "The parameters for the analysis were as follows: number of repetitions, 0 or 1; maximum number of motifs, 14; and optimum motif width, 6–100. The MAST program (Bailey and Gribskov, 1998) was used to search for each of the motifs in the AOP sequences. "
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