Alignment

blAffinealign() - Perform simple N&W alignment of seq1 and seq2 with separate gap opening and extension penalties
blAffinealignuc() - Perform simple N&W alignment of seq1 and seq2 with separate gap opening and extension penalties. Optimized for DNA sequences
blAlign() - Perform simple N&W alignment of seq1 and seq2. A single gap penalty is used so there is no extension penalty
blCalcMDMScore() - Calculates a score for comparing two amino acids using a mutation data matrix
blCalcMDMScoreUC() - As blCalcMDMScore() but upcases the amino acid labels before calculation
blNumericAffineAlign() - Perform simple N&W alignment using sequences encodede as arrays of numeric tokens
blNumericCalcMDMScore() - Calculate score from static globally stored mutation data matrix for number-encoded sequences
blNumericReadMDM() - Read mutation data matrix into static global arrays for number-encoded sequences
blReadMDM() - Read mutation data matrix into static global arrays for use by alignment code
blSetMDMScoreWeight() - Apply a weight to a particular amino acid substitution. Modifies the scoring matrix read by blReadMDM()
blZeroMDM() - Modifies all values in the MDM such that the minimum value is 0

Conversions

blDNAtoAA() - Converts a nucleic acid codon to the 1-letter amino acid equivalent. Termination codons are returned as X. No special action is taken for initiation codons.
blOnethr() - Converts 1-letter code to 3-letter code (actually as 4 chars).
blThrone() - Converts 3-letter code to 1-letter code. Handles ASX and GLX as X
blThronex() - Converts 3-letter code to 1-letter code. Handles ASX and GLX as B and Z.

File IO

blReadRawPIR() - This is based on ReadPIR(), but reads all characters into the sequence arrays (i.e. all punctuation characters are read as is). This is useful when punctuation has been used to indicate consensus sequence features.
blReadSimplePIR() - Read a PIR file containing multiple chains of up to maxres amino acids. Doesn't handle special PIR characters

Obtaining information

blKnownSeqLen() - Scans a 1-letter code sequence and calculate the length without `-', ` ' or '?' residues
blTrueSeqLen() - Scans a 1-letter code sequence and calculate the length without `-' or ` ' residues

Sequence manipulation

blBuildAAList() - Converts a sequence string into a linked list
blBuildFlagSeqFromAAList() - Builds a sequence string with blanks except where the flag in the sequence structure is set. At these positions the character specified in ch is used instead.
blBuildSeqFromAAList() - Converts the linked list back into a string which is malloc'd
blFindAAListItemByResnum() - Searches the linked list of the specified resnum (i.e. the original residue number in the sequence before any insertions were made) and returns a pointer to that item in the list.
blFindAAListOffsetByResnum() - Searches the linked list of the specified resnum (i.e. the original residue number in the sequence before any insertions were made) and returns the position of that residue in the list (numbered from 1)
blGetAAListLen() - Returns the number of items in the linked list
blInsertNextResidueInAAList() - Inserts a residues after the current position in the linked list. The returned value is the residue which has been inserted so this can be called again on the returned aa to insert another aa
blInsertNextResiduesInAAList() - Inserts a set of identical residues after the current position in the linked list. The returned value is the last residue which has been inserted so this can be called again on the returned aa to insert another aa
blInsertResidueInAAListAt() - Inserts a residue after the specified position in the list. Residues are numbered from 1. If the position is > length of the list then the residue will be added at the end. If the position is zero, it will be at the start of the list in which case the return value for the list will be different from the input value.
blInsertResiduesInAAListAt() - Inserts a set of residues after the specified position in the list. Residues are numbered from 1. If the position is > length of the list then the residue will be added at the end. If the position is zero, it will be at the start of the list in which case the return value for the list will be different from the input value.
blSetAAListFlagByResnum() - Searches the linked list of the specified resnum (i.e. the original residue number in the sequence before any insertions were made) and sets the flag in that item in the linked list

Note that there are also functions to extract sequence data from PDB files