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Programs for BPPS/SIPRIS analysis of protein domains. For further information contact: Prof. Andrew F. Neuwald Institute for Genome Sciences and Department of Biochemistry & Molecular Biology University of Maryland School of Medicine 801 West Baltimore St. BioPark II, Room 617 Baltimore, MD 21201 Tel: 410-706-6724; Fax: 410-706-1482 E-mail: aneuwald@som.umaryland.edu To compile the code simply type "./mkdrivers" within the src_code/ directory. This will create executables within the src_code/bin/ directory. WARNING: lex and yacc must be on your path for code compilation. If only flex and bison are available, then symbolic links (lex --> flex and yacc --> bison) may be set up instead. Literature references: 1. Neuwald, A.F. 2009. Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. Bioinformatics 25: 1869-1875 (Describes an initial version of the MAPGAPS program.) 2. Neuwald, A.F. 2011. Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms. Statistical Applications in Genetics and Molecular Biology 10(1): Article 36. (30 pages) (Describes a basic version of BPPS sampling). 3. Neuwald, A.F. 2014. A Bayesian sampler for optimization of protein domain hierarchies. Journal of Computational Biology 21(3): 269-286. (Describes the first step in the BPPS sampler used here). 4. Neuwald, A.F. 2014. Protein Domain Hierarchy Gibbs Sampling Strategies. Statistical Applications in Genetics and Molecular Biology 13(4):497-517. (Describes statistical aspects of BPPS sampling). 5. Neuwald, A.F., L. Aravind & S.F. Altschul. 2017. Inferring Joint Sequence-Structural Determinants of Protein Functional Specificity. eLife In revision. (Describes BPPS/SIPRIS analysis using the mapgaps, bpps & sipris programs.)
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