The project is a molecular biology computer Resource for the Northeastern United States, coupled with a Research program on computer pattern recognition in molecular genetics. The Research has two main objectives. One is to develop statistical and computer methods that can reveal syntactic and semantic patterns in DNA, RNA, and protein sequences, most of which are still obscure or unknown. The other is to use such pattern analysis tools - those developed in the course of the project and others that are deemed appropriate - to discover sequences that trace evolution and that regulate the expression of important genes and gene families. The identification of such sequences should provoke the formulation and testing of major hypotheses in molecular evolution, gene regulation and developmental genetics. The molecular biology computer Resource provides these DNA, RNA, and protein sequence analysis tools - and all others that are demonstrably valid and useful and freely available - to investigators within this region on-line, and to the larger research community on magnetic media. On-line access is through computers at the Resource site, and the programs distributed on tapes and floppy disks are for micro, supermicro, mini, and mainframe computers running under UNIX and other operating systems. The resource trains molecular biologists in statistics and computer methods, and educates biomathematicians and computer scientists in contemporary molecular genetics. Research opportunities combining these disciplines are offered yearly to postdoctoral fellows, and quarterly to visiting scientists. In addition, the Northeast and Los Alamos Resources (the Theoretical Biology and Biophysics Group, Los Alamos National Laboratory that is responsible for GenBank) will co-sponsor an international symposium on computer analysis in molecular evolution, gene regulation, and developmental genetics in 1985. The Northeast resource is committed to the principle of a Molecular Biology Network linking all regional computer resources in that field of science.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
1P41RR002275-01
Application #
3104092
Study Section
(BET)
Project Start
1985-04-01
Project End
1990-03-31
Budget Start
1985-04-01
Budget End
1986-03-31
Support Year
1
Fiscal Year
1985
Total Cost
Indirect Cost
Name
Dana-Farber Cancer Institute
Department
Type
DUNS #
149617367
City
Boston
State
MA
Country
United States
Zip Code
Lathrop, R H; Rogers Jr, R G; Smith, T F et al. (1998) A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment. Bull Math Biol 60:1039-71
Baxter, K; Steeg, E; Lathrop, R et al. (1996) From electron density and sequence to structure: integrating protein image analysis and threading for structure determination. Proc Int Conf Intell Syst Mol Biol 4:25-33
Lathrop, R H; Smith, T F (1996) Global optimum protein threading with gapped alignment and empirical pair score functions. J Mol Biol 255:641-65
White, J V; Stultz, C M; Smith, T F (1994) Protein classification by stochastic modeling and optimal filtering of amino-acid sequences. Math Biosci 119:35-75
Lathrop, R H (1994) The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng 7:1059-68
Lawler, J; Duquette, M; Urry, L et al. (1993) The evolution of the thrombospondin gene family. J Mol Evol 36:509-16
Smith, R F; Smith, T F (1992) Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. Protein Eng 5:35-41
Guigo, R; Johansson, A; Smith, T F (1991) Automatic evaluation of protein sequence functional patterns. Comput Appl Biosci 7:309-15
Zhu, Q L; Smith, T F; Lathrop, R H et al. (1990) Acid helix-turn activator motif. Proteins 8:156-63
Fischel-Ghodsian, F; Mathiowitz, G; Smith, T F (1990) Alignment of protein sequences using secondary structure: a modified dynamic programming method. Protein Eng 3:577-81

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