Home

SPSsearch

Usage: spssearch [-options] <queries FASTA file> <target FASTA file(s)>
  Available options are:
   -h            : print this brief help on version and usage
   -b <n>        : number of alignments (default 1); not changeable for now)
   -d <name>     : optioanl target file input method; position-independent
   -i <name>     : optional query file input; position-independent
   -sw           : (default) use Smith-Waterman algorithm for alignments
   -dasw         : use Double-Affine SW algorithm for alignments
   -tdo          : tab-delimited-output flag
   -M blosum<n>  : sets scoring matrix to blosum<n>, default blosum62
                   valid arguments: blosum35
                                    blosum45
                                    blosum62
                                    blosum80
                                    blosum100
   -p (t)blast<c>: sets search method (default blastp)
                                              Queries        Targets
                                             ---------      ---------
                   valid arguments: blastn  (DNA        vs        DNA)
                                    blastx  (trans DNA  vs   proteins)
                                    blastp  (proteins   vs   proteins)
                                   tblastn  (proteins   vs  trans DNA)
                                   tblastx  (trans DNA  vs  trans DNA)
   -q <n>        : nucleic/nucleic mismatch penalty (default -3)
   -G <n>        : gap initiation penalty (default -5)
                   overrides default blosum values: blosum35  -10
                                                    blosum45  -10
                                                    blosum62  -12
                                                    blosum80  -16
                                                    blosum100 -20
                   when set, otherwise blosum defaults used
   -E <n>        : gap extension penalty (default -2)
                   overrides default blosum values: blosum35  -1
                                                    blosum45  -1
                                                    blosum62  -2
                                                    blosum80  -1
                                                    blosum100 -1
                   when set, otherwise blosum defaults used
   -E2 <n>       : second gap extension penalty (default 0)
                   for double-affine SW, otherwise ignored
   -L2 <n>       : gap length at which second gap extension penalty
                   for double-affine SW becomes active (default 10)
   -S <n>        : complement queries? <n> = 1, no complements (default)
                                       <n> > 1, complement queries
   -minscore <n> : minimum SW score for showing  alignment (default 10)
   Note about SW implemenation: These versions of SW impose a gap-initiation
   penalty at the beginning of a gap and then impose the gap-extension penalty
   after that. A gap of 10 spaces will have a total negative score of
   gap-init + 9 * gap-extension.  Some versions of SW, notably Time-Logic's,
   impose the gap-initiation penalty and the gap-extension penalty in the first
   gap location. (A gap of 10 spaces would have a score of
   gap-initiation + 10 * gap-extension). Therefore, to replicate TL's SW you need
   to use a gap-initiation penalty which is smaller by the gap-extension penalty.