A method to identify specifity determining residues in protein families using Between Group Analysis
|Date of publication||None|
|Maintainer||Iain Wallace <email@example.com>|
add_pseudo_counts: Add pseudo counts to amino acid matrix based on defined...
amino_counts: calculate count of amino acid types at each position
average_cols_aap: Replaces gaps with the average of the column
bgafun: BGAfun A method to identify specifity determining residues in...
calculate_pseudo: Calculates pseudo count for each column in the amino acid...
Calculate_Row_Weights: Calculate the sequence weights for all the rows in my...
convertAAP.package: Converts an alignment into a matrix using the AAP encoding
convert_aln_AAP: Converts alignment into a matrix using the amino acid...
convert_aln_amino: Converts an alignment object into binary amino matrix
convert_amino.package: The functions required to convert an alignment into a binary...
convert_seq_AAP: Convert sequence into string representing AAP values
convert_seq_amino: Converts a single seqeunce into a binary string
create_colnames_AAP: Create column names for an AAP matrix
create_colnames_amino: Creates the column names for the binary matrix
create_probab: Generates probability matrix for pseudocounts calculation
create_profile: Creates a sequence profile for an binary amino acid matrix
create_profile_strings: Create a profile string for each group in an alignment
Henikoff_weights: Calculates Henikoff weights for each sequence in a binary...
LDH: LDH alignment read in from a file
LDH.aap: AAP matrix
LDH.aap.ave: AAP matrix
LDH.amino: Binary amino acid matrix after converting the Lactate...
LDH.amino.gapless: Amino acid matrix after removing gaps
LDH.amino.pseudo: Amino acid matrix after adding pseudo counts
LDH.groups: Groups in the LDH alignment
pseudo_counts: Calculate pseudo counts for a profile
remove_gaps: Removes gaps from a amino binary matrix
remove_gaps_groups: remove gaps from a binary amino matrix
run_between_pca: run PCA to identify functional positions in an alignment
sum_20_aln: Calculates number of amino acids in each group of 20 columns...
sum_20_cols: Calculate number of amino acids in a column of an alignment
sum_aln: Calculate number of amino acids in each position in an...
top_residues_2_groups: Return a list of the top residues at either end of the axis
Weight_Amino: Calculates sequence weight for each sequence in an amino acid...