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).