NAME

       SIBsim4 - align RNA sequences with a DNA sequence, allowing for introns

SYNOPSIS

       SIBsim4 [ options ] dna rna_db

DESCRIPTION

       SIBsim4  is a similarity-based tool for aligning a collection of expressed sequences (EST,
       mRNA) with a genomic DNA sequence.

       Launching SIBsim4 without any arguments will print the  options  list,  along  with  their
       default values.

       SIBsim4  employs  a  blast-based  technique  to  first determine the basic matching blocks
       representing the "exon cores".  In this first stage, it detects all possible exact matches
       of  W-mers  (i.e.,  DNA  words  of  size  W) between the two sequences and extends them to
       maximal scoring gap-free segments.  In the second stage, the exon cores are extended  into
       the  adjacent as-yet-unmatched fragments using greedy alignment algorithms, and heuristics
       are used to favor configurations that  conform  to  the  splice-site  recognition  signals
       (e.g., GT-AG). If necessary, the process is repeated with less stringent parameters on the
       unmatched fragments.

       By default, SIBsim4 searches both strands and reports the best matches,  measured  by  the
       number  of  matching nucleotides found in the alignment.  The R command line option can be
       used to restrict the search to one orientation (strand) only.

       Currently, four major alignment display options are supported, controlled by the A option.
       By  default,  only  the  endpoints, overall similarity, and orientation of the introns are
       reported. An arrow sign ('->' or '<-') indicates the orientation of the intron.  The  sign
       `==' marks the absence from the alignment of a cDNA fragment starting at that position.

       In  the description below, the term MSP denotes a maximal scoring pair, that is, a pair of
       highly similar fragments in the two sequences, obtained during the blast-like procedure by
       extending a W-mer hit by matches and perhaps a few mismatches.

OPTIONS

       -A <int>
              output format
                0: exon endpoints only
                1: alignment text
                3: both exon endpoints and alignment text
                4: both exon endpoints and alignment text with polyA info

              Note that 2 is unimplemented.

              Default value is 0.

       -C <int>
              MSP score threshold for the second pass.

              Default value is 12.

       -c <int>
              minimum  score cutoff value.  Alignments which have scores below this value are not
              reported.

              Default value is 50.

       -E <int>
              cutoff value.

              Default value is 3.

       -f <int>
              score filter in percent.  When multiple hits are detected for the same RNA element,
              only  those having a score within this percentage of the maximal score for that RNA
              element are reported.  Setting this value to 0 disables filtering and all hits will
              be reported, provided their score is above the cutoff value specified through the c
              option.

              Default value is 75.

       -g <int>
              join exons when gap on genomic and RNA have lengths which differ at  most  by  this
              percentage.

              Default value is 10.

       -H <int>
              report  chimeric  transcripts  when the best score is lower than this percentage of
              the overall RNA coverage and the chimera score is greater than this  percentage  of
              the RNA length (0 disables this report)

              Default value is 75.

       -I <int>
              window width in which to search for intron splicing.

              Default value is 6.

       -K <int>
              MSP score threshold for the first pass.

              Default value is 16.

       -L <str>
              a comma separated list of forward splice-types.

              Default value is "GTAG,GCAG,GTAC,ATAC".

       -M <int>
              scoring splice sites, evaluate match within M nucleotides.

              Default value is 10.

       -o <int>
              when printing results, offset nt positions in dna sequence by this amount.

              Default value is 0.

       -q <int>
              penalty for a nucleotide mismatch.

              Default value is -5.

       -R <int>
              direction of search
                0: search the '+' (direct) strand only
                1: search the '-' strand only
                2: search both strands

              Default value is 2.

       -r <int>
              reward for a nucleotide match.

              Default value is 1.

       -S <int>
              splice site indels search breadth.  While determining the best position of a splice
              site, SIBsim4 will evaluate adding at most this number of insertions and  deletions
              on the DNA strand on each side of the splice junction.

              Default value is 2.

       -s <int>
              split  score  in  percent.   While  linking  MSP, if two consecutive group of exons
              appear like they could be part of two different copies of the same gene, they  will
              be tested to see if the score of each individual group relative to the best overall
              score is greater than this value.  If both groups have a relative score above  this
              threshold they will be split.

              Default value is 75.

       -W <int>
              word size.

              Default value is 12.

       -X <int>
              value for terminating word extensions.

              Default value is 12.