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An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences (1990)

Lawrence, Charles E. ; Reilly, Andrew A.

New York, NY : Wiley-Blackwell

Proteins: Structure, Function, and Genetics 7 (1990), S. 41-51

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ISSN: 0887-3585

Keywords: DNA binding proteins ; maximum likelihood ; CRP ; finite mixtures ; transcription regulation ; Chemistry ; Biochemistry and Biotechnology

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Medicine

Notes: Statistical methodology for the identification and characterization of protein binding sites in a set of unaligned DNA fragments is presented. Each sequence must contain at least one common site. No alignment of the sites is required. Instead, the uncertainty in the location of the sites is handled by employing the missing information principle to develop an “expectation maximization” (EM) algorithm. This approach allows for the simultaneous identification of the sites and characterization of the binding motifs. The reliability of the algorithm increases with the number of fragments, but the computations increase only linearly. The method is illustrated with an example, using known cyclic adenosine monophophate receptor protein (CRP) binding sites. The final motif is utilized in a search for undiscovered CRP binding sites.

Additional Material: 3 Ill.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1002/prot.340070105

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Habituation of Activity in an Open Field: A Survey of Inbred Strains and F1 Hybrids (2000)

Bolivar, Valerie J. ; Caldarone, Barbara J. ; Reilly, Andrew A. ; [et al.]

Springer

Behavior genetics 30 (2000), S. 285-293

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ISSN: 1573-3297

Keywords: Inbred strains ; habituation ; open-field activity

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Psychology

Notes: Abstract To determine if there is genetic variability in habituation of activity in an open field, we examined a number of inbred strains and F1 hybrids. Using 5-min exposures to a dark open field, we measured changes in exploratory behavior over 3 consecutive days in 129S3/SvImJ, A/J, BALB/ cByJ, C3H/HeJ, C57BL/6J, CBA/J, DBA/2J, FVB/NJ, (B6 × 129)F1/J, and (B6 × C3H) F1/J male and female mice. Strain differences in open-field activity and in habituation were evident. Some of the strain differences were further modified by sex. The strains and F1's could be separated into groups that increased, decreased, or did not modify their activities across testing sessions. In a second study, the effects of altering the floor surface on habituation were examined in male 129S3/SvImJ, C57BL/6J, DBA/2J, and (B6 × 129)F1/J mice. When the floor was altered after 3 consecutive days of habituation, increased activity levels were evident. There were strain differences in the responsiveness to the changes in the floor. These results confirm a genetic role in intersession habituation to an open field.