libseqaln
NAME
libseqaln - Library of sequence alignment functions
DESCRIPTION
#include seqaln.h
append_score
Append a position ( i,j ) to a traceback list
asc2num Convert an ASCII letter to a number, 0--26
bcd2num Convert an EBCDIC letter to a number, 0--26
(untested)
bestincol Find the best score in a given matrix column
bestinrow Find the best score in a given matrix row
brkpt Empty breakpoint routine, used for debugging
code2seq Rebuild the seq part of sequence structure from
the code part
compseq Replace sequence with its complement
delta Score function for match or mismatch of a letter
pair
fddeclump Fit distance declumping
find Forward spaces in a file to find a fixed pattern
fitD Fit distance scoring
fitS Fit similarity scoring
fsdeclump Fit similarity declupming
gap Score function for indel gap of a given length
gb2fasta Converts a Genbank-format sequence entry into
FASTA format
genalign Generate a pair of alignment sequences from a dis-
tribution
getbest Get the min score for distance, max for similarity
getmaxS Get maximum score in a scoring matrix, for local
alignment
getminS Get minimum score in a scoring matrix
getpvalue Determine gamma and p given a histogram of high
scores
gettop Find the top score in a 26 by 26 scoring matrix
globalD Global distance scoring
globalS Global similarity scoring
grow_seq Increases the memory allocated for handling
sequences from a database
initmaxS Initialize vector of best score possible in a
row/column
linreg Linear regression fitting double-precision arrays
x and y
load_db Loads the first sequence in a database of
sequences in FASTA format
load_distrib
Load a frequency distribution file
load_mat Load a 26 by 26 penalty matrix
load_pro Load a comparison profile
load_seq Load a sequence
localS Local similarity scoring
lsdeclump Local similarity declumping
make_seq Generate a sequence following a frequency distri-
bution
markdiag Mark all aligned pairs in a traceback, for
declumping
markseq Mark sequence positions as aligned, for tandem
repeats
max Maximum of two numbers
max3 Maximum of three numbers
mdelta Matrix scoring function to match one letter with
another
memfree Free memory allocated by the sequence library
software
min Minimum of two numbers
min3 Minimum of three numbers
newmem Allocate new memory; print error message upon
error
nextpval Determine next P( score_k > t ), for p-value
software
next_seq Loads the pending sequence in a database of
sequences in FASTA format
overS Overlap similarity alignment
parseargs Parse arguments and flags to all standalone pro-
grams
pdelta Profile scoring function to match a letter with a
profile
pfitS Profile fit similarity scoring
pfsdeclump
Profile fit similarity declumping
pgap Scoring function to score an indel gap in a pro-
file
pir2fasta Converts a PIR-format sequence entry into FASTA
format
print_trace
Print a traceback coordinate list
prpt_row Report one row of scores with profile comparison
ptrace Perform a traceback for a profile scoring matrix
pvlocalS P-value simulation for local similarity alignment
results_init
Allocate and initialize results structure
revcomp Replace sequence with its reverse-complement
reverse_list
Reverse the order of a traceback linked list
revseq Replace sequence with its reverse
rpt_alignment
Report the alignment associated with a traceback
rpt_row Report one row of scores from a normal scoring
matrix
rpt_scores
Report the scoring matrix
rpt_version
Print the version number of the sequence alignment
library
scandiag Check if a match or mismatch occurs during trace-
back
scanleft Check if indel to the left occurs during traceback
scanup Check if indel upwards occurs during traceback
sp2fasta Converts a Swissprot-format sequence entry into
FASTA format
srgetmaxS Get max score in self-repeat (lower-triangular)
matrix
srlocalS Self-repeat local similarity scoring
srlsdeclump
Self-repeat local similarity declumping
topscore Find the highest score in a 26 by 26 penalty
matrix
trace Perform an ordinary traceback
trlocalS Tandem repeat (wraparound) local similarity scor-
ing
trlsdeclump
Tandem repeat local similarity declumping
trrpt_alignment
Print alignment from a tandem-repeat traceback
trrpt_scores
Print scoring matrix for a tandem-repeat
trtrace Print traceback list from a tandem-repeat trace-
back
SEE ALSO
seqaln-intro(1).