SIBsim4(1)							   User Manuals 							SIBsim4(1)

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  neces-
       sary, 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 align-
       ment.  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 similar-
       ity,  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.

Bioinformatics							    April 2007								SIBsim4(1)