1SIBsim4(1) User Manuals SIBsim4(1)
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6 SIBsim4 - align RNA sequences with a DNA sequence, allowing for introns
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9 SIBsim4 [ options ] dna rna_db
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12 SIBsim4 is a similarity-based tool for aligning a collection of
13 expressed sequences (EST, mRNA) with a genomic DNA sequence.
14 Launching SIBsim4 without any arguments will print the options list,
16 along with their default values.
17 SIBsim4 employs a blast-based technique to first determine the basic
19 matching blocks representing the "exon cores". In this first stage, it
20 detects all possible exact matches of W-mers (i.e., DNA words of size
21 W) between the two sequences and extends them to maximal scoring gap-
22 free segments. In the second stage, the exon cores are extended into
23 the adjacent as-yet-unmatched fragments using greedy alignment algo‐
24 rithms, and heuristics are used to favor configurations that conform to
25 the splice-site recognition signals (e.g., GT-AG). If necessary, the
26 process is repeated with less stringent parameters on the unmatched
27 fragments.
28 By default, SIBsim4 searches both strands and reports the best matches,
30 measured by the number of matching nucleotides found in the alignment.
31 The R command line option can be used to restrict the search to one
32 orientation (strand) only.
33 Currently, four major alignment display options are supported, con‐
35 trolled by the A option. By default, only the endpoints, overall simi‐
36 larity, and orientation of the introns are reported. An arrow sign
37 ('->' or '<-') indicates the orientation of the intron. The sign `=='
38 marks the absence from the alignment of a cDNA fragment starting at
39 that position.
40 In the description below, the term MSP denotes a maximal scoring pair,
42 that is, a pair of highly similar fragments in the two sequences,
43 obtained during the blast-like procedure by extending a W-mer hit by
44 matches and perhaps a few mismatches.
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48 -A <int>
49 output format
50 0: exon endpoints only
51 1: alignment text
52 3: both exon endpoints and alignment text
53 4: both exon endpoints and alignment text with polyA info
54 Note that 2 is unimplemented.
56 Default value is 0.
58 -C <int>
60 MSP score threshold for the second pass.
61 Default value is 12.
63 -c <int>
65 minimum score cutoff value. Alignments which have scores below
66 this value are not reported.
67 Default value is 50.
69 -E <int>
71 cutoff value.
72 Default value is 3.
74 -f <int>
76 score filter in percent. When multiple hits are detected for
77 the same RNA element, only those having a score within this per‐
78 centage of the maximal score for that RNA element are reported.
79 Setting this value to 0 disables filtering and all hits will be
80 reported, provided their score is above the cutoff value speci‐
81 fied through the c option.
82 Default value is 75.
84 -g <int>
86 join exons when gap on genomic and RNA have lengths which differ
87 at most by this percentage.
88 Default value is 10.
90 -H <int>
92 report chimeric transcripts when the best score is lower than
93 this percentage of the overall RNA coverage and the chimera
94 score is greater than this percentage of the RNA length (0 dis‐
95 ables this report)
96 Default value is 75.
98 -I <int>
100 window width in which to search for intron splicing.
101 Default value is 6.
103 -K <int>
105 MSP score threshold for the first pass.
106 Default value is 16.
108 -L <str>
110 a comma separated list of forward splice-types.
111 Default value is "GTAG,GCAG,GTAC,ATAC".
113 -M <int>
115 scoring splice sites, evaluate match within M nucleotides.
116 Default value is 10.
118 -o <int>
120 when printing results, offset nt positions in dna sequence by
121 this amount.
122 Default value is 0.
124 -q <int>
126 penalty for a nucleotide mismatch.
127 Default value is -5.
129 -R <int>
131 direction of search
132 0: search the '+' (direct) strand only
133 1: search the '-' strand only
134 2: search both strands
135 Default value is 2.
137 -r <int>
139 reward for a nucleotide match.
140 Default value is 1.
142 -S <int>
144 splice site indels search breadth. While determining the best
145 position of a splice site, SIBsim4 will evaluate adding at most
146 this number of insertions and deletions on the DNA strand on
147 each side of the splice junction.
148 Default value is 2.
150 -s <int>
152 split score in percent. While linking MSP, if two consecutive
153 group of exons appear like they could be part of two different
154 copies of the same gene, they will be tested to see if the score
155 of each individual group relative to the best overall score is
156 greater than this value. If both groups have a relative score
157 above this threshold they will be split.
158 Default value is 75.
160 -W <int>
162 word size.
163 Default value is 12.
165 -X <int>
167 value for terminating word extensions.
168 Default value is 12.
170Bioinformatics April 2007 SIBsim4(1)