CreateConservationPSP

! Attention - update on August 04, 2020

Dear user,
The functionality of this application is not open for public use yet. Please be patient. If you have questions in the meantime, please contact us by sending an email.

CreateConservationPSP is an algorithm based on suffix trees to efficiently compute an alignment-free conservation-based PSP score over locations in a DNA sequence. The PSP score is computed based on counting how many times a DNA site is conserved in orthologous sequences, irrespective of orientation or location in these sequences.

Using the conservation-based PSP in MotifSampler will favor the detection of motifs in a reference species that are well conserved in related species over those that are not.
Although NOMS and PHMS already take orthology into account by design, using a PSP build on conservation counts from a subset of close orthologs will guide towards better initial seeds that benefit the motif detection in distant orthologs.
In other words, the use of a conservation-based PSP in PHMS and NOMS can be seen as a "soft" prealignment of sequences.

To optimally run the tool and evaluate its output, please consult the guidelines. Optionally, read the results of a Case study : Improved motif detection performance of MotifSampler on real benchmark datasets when using a conservation-based PSP for the detection of motifs well conserved in close orthologs.

The speed with which results are generated depends on the server load.

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Run CreateConservationPSP:

To run this application, please fill in the required input in the blank fields. In the output section, a (randomized) file name has been generated. You can overwrite this automatically generated filename with a more meaningful description if desired (do not use spaces, dots, colons,... in this name). The program parameters have been set to a default value. Please analyze if these settings apply to your case (checkout our Guidelines) and overwrite whenever needed. Pressing Submit will initiate the selected software on our server. An url containing the results will be sent by email.
Illustrative examples are the result of running CreateConservationPSP on orthologous sequences from yeast (Saccharomyces species) containing known binding sites for the Urs1h transcription factor.

Input:
Your email address, we will mail you the url with the result.
-f <filename>: file with orthologous DNA sequences in Fasta format (Urs1h example)

Output:
-o <filename>: file with conservation-based PSP over DNA start positions (PSP format, Urs1h example)

Parameters:
-r <name>: Description of the reference species for which the PSP values must be reported. Default the first listed species is selected: <first>. To optionally report PSP for all species: type <all>
-w <value>: length of the conserved DNA segment. Default <10>.
-s <0\|1>: default <1> both strands of the sequences will be analyzed (i.e. input sequences and the reverse complement). <0> is only input sequences.
-x <value>: maximum number of unidentified nucleotides ('N') allowed in a conserved DNA segment. Default <1>.
Proceed with carefully evaluating the generated PSP file. You may want to omit PSP information for one or more sets of sequences before proceeding with Gibbs sampling based motif detection.