Better ALignment CONsensus analYsis


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Documentation for package ‘BALCONY’ version 0.2.10

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alignment Sample alignment of soluable epoxide hydrolase family
alignment2matrix Load alignment into matrix
align_params Get alignment dimensions
align_seq_mtx2grs Convert amino acid symbols to groups according to their properties of user's choice.
barplotshow Shows barplot with amino acid variation on the specified position
calculate_AA_variation Calculate AA variations on each position of the multiple sequence alignment
calculate_pseudo_counts Calculate pseudo counts for alignment
compare_cons_metrics compare_cons_metrics
cons2seqs_ident Identity of each sequence in the alignment to the consensus sequence.
cons2seqs_sim Group consensus to each sequence in the alignment similarity
consensus Consensus sequence determination
convert_AA_symbol Amino acids symbols conversion
create_final_CSV Create CSV file to save results
create_structure_seq Superimpose structural data of interest on sequence after the alignmment
CRE_conservativity Calculate cumulative relative entropy score
delete_isoforms Delete protein isoforms from alignment object
D_matrix Calculate substitution rate matrix between two amino acids
Escore_conservativity Calculate the Escore conservation metric
excl_low_prob_strcts Exclude low probability structural data
find_consecutive_seq Find sequences of numbers in a numeric vector
find_seq Find sequence by id in alignment.
find_seqid Find sequence identifier by other sequence identifier in given alignment within a specified library
get_pos_based_seq_weights Get position based weights of sequences in alignment
get_prot_entropy Get MSA-based calculated entropy for chosen protein.
get_remarks465_pdb Get "REMARK 465" data from PDB file
get_seq_names Get names of sequences from alignment
get_seq_weights Get sequences weights
get_structures_entropy Get entropy of amino acids (for region of interest) in given protein
get_structures_idx Get IDs of structure(s) elements from aligned sequences (MSA)
gonnet Gonnet substitution matrix
is_upper Check if the letter is uppercase.
kabat_conservativity Calculate Kabat conservation metric
kolmogorov_smirnov_test Perform Kolmogorov-Smirnov test for structural data
landgraf_conservativity Calculate Landgraf conservation score
noteworthy_seqs Find noteworthy sequences in the dataset (aligned sequences)
pairwise_alignment_MSA Calculate pairwise alignment for whole MSA
plot_entropy Plot entropies for protein
plot_structure_on_protein Plot structure entropy on protein background
prepare_structure_profile This function combines the entropy data for structure building amino acids with their indices
preprocess_hmm_output preprocess HMM output
read_structure Read structure data from a text file
RealValET_conservativity Calculate real-value Evolutionary Trace (ET)
schneider_conservativity Calculate Schneider conservation metric
shannon_conservativity Calculate Shannon conservation metric
small_alignment Sample small alignment of soluable epoxide hydrolase family
structure A sample structure data
substitution_mtx Read a substitution matrix