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... |
barplotshow | Shows barplot with amino acid variation on the specified... |
calculate_AA_variation | Calculate AA variations on each position of the multiple... |
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... |
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... |
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... |
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... |
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... |
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 |
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