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大肠杆菌基因数据集

大肠杆菌基因数据集

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Data Set Information:The data was collected from several sources, including GenProtEC ([Web link]) and SWISSPROT ([Web l......

数据结构 ? 73.28M

    Data Structure ?

    * 以上分析是由系统提取分析形成的结果,具体实际数据为准。

    README.md


    Data Set Information:

    The data was collected from several sources, including GenProtEC ([Web link]) and SWISSPROT ([Web link]). Structure prediction was made by PROF ([Web link]). Homology search was provided by PSI-BLAST ([Web link]).

    The data is in Datalog format. Missing values are not explicit, but some genes have more relationships than others.

    E. coli genes (ORFs) are related to each other by the predicate ecoli_to_ecoli(EcoliNumber,E-value,Psi-blast_iteration). 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(EcoliNumber)).
    end(model(EcoliNumber)).

    The gene functional classes are in a hierarchy. See [Web link] (note: the classes may have changed since original data collection).

    There are two datalog files: ecoli_data.pl and ecoli_functions.pl

    1. ecoli_functions.pl

    Lists classes and ORF functions. Lines are of the following form:

      class(5,1,1,'Colicin-related functions').
      class(5,1,'Laterally acquirred elements').
      class(5,'Extrachromosomal').

    Arguments are up to 3 numbers (describing class at up to 3 different levels), followed by a string class description. For example:

      function(ecoli210,7,0,0,'b0217','putative aminopeptidase').

    Arguments are ORF number, exactly 3 class numbers, gene name (or blattner number if no gene name), ORF description.

    2. ecoli_data.pl

    Data for each ORF (gene) is delimited by

      begin(model(ecoliX)).
      end(model(ecoliX)).

    where X is the ORF number. Other predicates are as follows (examples):
      ecoli_orf(ecoliX).    % X is ORF number
      ecoli_mol_wt(176624.1).  % float
      ecoli_theo_pI(5.81).     %float
      ecoli_atomic_comp(c,7940).   % {c,h,n,o,s} , int
      ecoli_aliphatic_index(69.57). % float
      ecoli_hydro(-0.549).          % float
      sec_struc(1,c,2).           % int (start), {a,b,c}, int (length)
      sec_struc_coil(1,2).        % int (start), int (length)
      sec_struc_beta(1,5).        % int (start), int (length)
      sec_struc_alpha(1,7).       % int (start), int (length)
      sequence_length(255).       % int
      amino_acid_ratio(a,8.9).    % amino_acid_char, float
      amino_acids(ecoli3013,a,70). % ORF_num, amino_acid_char, int
      amino_acid_pair_ratio(a,a,9.0). % amino_acid_char, amino_acid_char, float
      amino_acid_pairs(a,a,7).    % amino_acid_char, amino_acid_char, int
      ecoli_to_ecoli(1170,1.0e-105,5).  % ORF_num, double (e-value), int (iteration)
      e_val(o42893,2.0e-99).  % accession_number, double (e-value)
      psi_iter(o42893,5).     % accession_number, int (iteration)
      species(p52494,'candida_albicans__yeast_').  % accession_number, string
      mol_wt(p52494,104022). % accession_number, int
      classification(p52494,candida).  % accession_number, name
      keyword(p25195,'plasmid').   % accession_number, string

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