Man pages for BALCONY
Better ALignment CONsensus analYsis

aligned_sequences_matrix2groupsConvert amino acid symbols to groups according to their...
alignmentSample alignment of soluable epoxide hydrolase family
alignment2matrixLoad alignment into matrix
alignment_parametersGet alignment dimensions
barplotshowShows barplot with amino acid variation on the specified...
calculate_AA_variationCalculate AA variations on each position of the multiple...
cons2seqs_identIdentity of each sequence in the alignment to the consensus...
cons2seqs_simGroup consensus to each sequence in the alignment similarity
consensusConsensus sequence determination
convert_AA_symbolAmino acids symbols conversion
create_final_csvCreate CSV file to save results
create_structure_seqSuperimpose structural data of interest on sequence after the...
delete_isoformsDelete protein isoforms from alignment object
D_matrixCalculate substitution rate matrix between two amino acids
Escore_conservativityCalculate the Escore conservation metric
exclude_low_probability_structuresExclude low probability structural data
find_consecutive_seqFind sequences of numbers in a numeric vector
find_seqFind sequence by id in alignment.
find_seqidFind sequence identifier by other sequence identifier in...
get_prot_entropyGet MSA-based calculated entropy for chosen protein.
get_remarks465_pdbGet "REMARK 465" data from PDB file
get_seq_namesGet names of sequences from alignment
get_structures_entropyGet entropy of amino acids (for region of interest) in given...
get_structures_idxGet IDs of structure(s) elements from aligned sequences (MSA)
gonnetGonnet substitution matrix
is_upperCheck if the letter is uppercase.
kabat_conservativityCalculate Kabat conservation metric
kolmogorov_smirnov_testPerform Kolmogorov-Smirnov test for structural data
landgraf_conservativityCalculate Landgraf conservation score
noteworthy_sequencesFind noteworthy sequences in the dataset (aligned sequences)
plot_entropyPlot entropies for protein
plot_structure_on_proteinPlot structure entropy on protein background
prepare_structure_profileThis function combines the entropy data for structure...
read_structureRead structure data from a text file
schneider_conservativityCalculate Schneider conservation metric
shannon_conservativityCalculate Shannon conservation metric
small_alignmentSample small alignment of soluable epoxide hydrolase family
structureA sample structure data
substitution_mtxRead a substitution matrix
BALCONY documentation built on Nov. 29, 2017, 1:02 a.m.