SPatt 2.0 (Statistics for Patterns)
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http://stat.genopole.cnrs.fr/spatt

SPatt is a command-line program dedicated to the study of pattern occurrences in Markovian sequences. SPatt uses efficient automata (DFA) to treat any complex pattern and produce p-values with a wide range of statistical methods: from exact ones (FMCI, waiting times) to asymptotic approximations (Gaussian, binomial, Poisson, large deviations).

The aim of SPatt is to provide higly efficient state-of-the-art implementation for most (if not all) practical approaches to patternin random sequences.

Here is a couple of example of command line using SPatt:

$ spatt -a ab -p "aba.(0-3)baa" -m -1 --dfa dfa.dot

compute the DFA corresponding to the pattern "aba.(0-3)baa" (in the Graphviz's dot format) and output the corresponding PMC in the file "pmc.sci".

$ dot -Grankdir=LR -Nfontsize=40 -Efontsize=40 -Tps dfa.dot -o dfa.eps && gv dfa.eps

will let you see a graphical representation of the DFA (note that you need to get the Graphviz package - http://graphviz.org - in order to do this).

$ ./src/spatt -a ab -p "aba.(0-3)baa" -m -1 -S data/ab1000.fasta
distribution:
P(N=0)=1.451793e-24
P(N=1)=8.311068e-23
[output truncated]
P(N=39)=8.389673e-03
P(N>=40)=9.733052e-01
pattern=aba.(0-3)baa    Nobs=39 P(N<=Nobs)=2.669477e-02

gives the exact distribution of the pattern

$ spatt -a ab -p "aba.(0-3)baa" -m -1 -S data/ab1000.fasta --repartition
16      6.137695e-01    1
51      1.918259e-01    1
66      3.837891e-01    1
101     1.918259e-01    1
116     3.837891e-01    1
[output truncated]
951     1.918259e-01    1
966     3.837891e-01    1
1000    1.918259e-01    0

gives the occurrence positions and associate a waiting time p-value to each observation.

$ spatt -a ab -p "aba.(0-3)baa" -m -1 -S data/ab1000.fasta --gaussian
pattern=aba.(0-3)baa    Nobs=39 mean=52.402344  sd=6.872593     z-score=-1.950115       P(N<=Nobs)=2.558123e-02

performs a Gaussian approximation.

Please note that it is possible to use order m>=0 Markov model but, unlike SPatt branch 1.x, the parameter must be provided through the "-M" option. If you want to use parameter estimated over a sequence, the simplest way to do this is to use SPatt banch 1.x to perform the estimation.

Here is an example: DNA pattern "g.tggtgg.(0-12)g.tggtgg" on Escherichia coli K12 complete genome

$ sspatt U00096.fna -m 3 -M tmp.markov
$ spatt -a acgt -p "g.tggtgg.(0-20)g.tggtgg" -m 3 -M tmp.markov -S U00096.fna --gaussian --over
pattern=g.tggtgg.(0-20)g.tggtgg Nobs=14 mean=2.173635   sd=1.510378     z-score=7.830070