Man pages for BALCONY
Better ALignment CONsensus analYsis

alignmentSample alignment of soluable epoxide hydrolase family
alignment2matrixLoad alignment into matrix
align_paramsGet alignment dimensions
align_seq_mtx2grsConvert amino acid symbols to groups according to their...
barplotshowShows barplot with amino acid variation on the specified...
calculate_AA_variationCalculate AA variations on each position of the multiple...
calculate_pseudo_countsCalculate pseudo counts for alignment
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...
CRE_conservativityCalculate cumulative relative entropy score
delete_isoformsDelete protein isoforms from alignment object
D_matrixCalculate substitution rate matrix between two amino acids
Escore_conservativityCalculate the Escore conservation metric
excl_low_prob_strctsExclude 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_pos_based_seq_weightsGet position based weights of sequences in alignment
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_seq_weightsGet sequences weights
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_seqsFind noteworthy sequences in the dataset (aligned sequences)
pairwise_alignment_MSACalculate pairwise alignment for whole MSA
plot_entropyPlot entropies for protein
plot_structure_on_proteinPlot structure entropy on protein background
prepare_structure_profileThis function combines the entropy data for structure...
preprocess_hmm_outputpreprocess HMM output
read_structureRead structure data from a text file
RealValET_conservativityCalculate real-value Evolutionary Trace (ET)
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 July 21, 2018, 1:01 a.m.