The data was collected from several sources, including the Sanger Centre (http://www.sanger.ac.uk/Projects/M_tuberculosis/Gene_list/) and SWISSPROT (http://www.expasy.ch/sprot/sprot-top.html). Structure prediction was made by PROF (http://www.aber.ac.uk/~phiwww/prof/index.html). Homology search was made by PSI-BLAST (http://www.ncbi.nlm.nih.gov/BLAST/). The data is in Datalog format. Missing values are not explicit, but some genes have more relationships than others. Dependencies: M. tuberculosis genes (ORFs) are related to each other by the predicate tb_to_tb_evalue(TBNumber,E-value). They are related to other (SWISSPROT) proteins by the predicate e_val(AccNo,E-value). All the data for a single gene (ORF) is enclosed between delimiters of the form: begin(model(TBNumber)). end(model(TBNumber)). Other Relevant Information: The gene functional classes are in a hierarchy. See http://www.sanger.ac.uk/Projects/M_tuberculosis/Gene_list/. There are two datalog files: tb_data.pl and ecoli_functions.pl 1. tb_functions.pl Lists classes and ORF functions. Lines are of the following form: class([1,0,0,0],"Small-molecule metabolism "). class([1,1,0,0],"Degradation "). class([1,1,1,0],"Carbon compounds "). Arguments are a list of 4 numbers (describing class at the 4 different levels), followed by a string class description. For example, function(tb186,[1,1,1,0],'bglS',"beta-glucosidase"). Arguments are ORF number, list of 4 class numbers, gene name (or null if no gene name) in single quotes, ORF description in double quotes. 2. tb_data.pl Data for each ORF (gene) is delimited by begin(model(X)). end(model(X)). where X is the ORF number. Other predicates are as follows (examples): tb_protein(X). % X is gene number function(2,1,5,0,'gyrA','DNA gyrase subunit A'). % 4 levels of functional hierarchy, gene name, description coding_region(7302,9815). % start,end. integers tb_mol_wt(19934). % integer access(1,e,20). % int (position), {e,i,b}, int (length) access_exposed(1,20). % int (position), int (length) access_intermediate(26,1). % int (position), int (length) access_burried(1,2). % int (position), int (length) access_dist(b,42.8). % {e,i,b}, float (percentage) sec_struc(1,c,23). % int (position), {a,b,c}, int (length) sec_struc_coil(1,23). % int (position), int (length) sec_struc_alpha(1,15). % int (position), int (length) sec_struc_beta(1,6). % int (position), int (length) struc_dist(a,32.1). % {a,b,c}, float (percentage) sec_struc_conf(78.8). % float (confidence) sec_struc_conf_alpha(88.9). % float (confidence) sec_struc_conf_beta(58.0). % float (confidence) sec_struc_conf_coil(77.7). % float (confidence) psi_sequences_found(1,7). % how many found, which iteration psi_sequences_found_again(2,7). % how many found, which iteration psi_sequences_found_new(2,0). % how many found, which iteration amino_acid_ratio(a,11.2). % amino acid letter, float amino_acid_pair_ratio(a,c,0.0). % amino acid letter, amino acid letter, float (out of 1000, ie 2.8 = 0.28%) sequence_length(187). % integer tb_to_tb_evalue(tb3671,1.100000e-01). % ORF number, e-value (double) e_val(p35925,7.0e-59). % SWISSPROT accession no, e-value (double) species(p35925,'streptomyces_coelicolor'). % SWISSPROT acc no, string classification(p35925,bacteria). % SWISSPROT acc no, name mol_wt(p35925,19772). % SWISSPROT acc no, integer keyword(p35925,'hypothetical_protein'). % SWISSPROT acc no, string db_ref(p35925,embl,l27063,g436026,null). % SWISSPROT acc no, db id, primary id, secondary id, status id signalip(c,35,no). % {c,y,s}, int (signal peptide c/y/s score), yes/no signalip(ss,1,34,no). % ss, int, int, yes/no signalip(cleavage,59,60). % cleavage, int/null, int/null hydro_cons(-0.498,-0.474,0.624,3.248,0.278). % double, double, double, double, double gene_name(p41514,'gyrb'). % SWISSPROT acc no, string

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