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Frequently asked questions: The SSA Web Site

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General Questions

Is there a standalone version of SSA?

Unfortunately we do not provide a standalone version of SSA. The software relies on local libraries and so is not easy to make it run on other machines.

What's the meaning of PWMs on this Server?

The formula we use to derive the PWM is the following, each element of the matrix, designated by PWMij (i=1,2,3,4, for A, C, G, T, and j is the site index) is given by:

  • PWMij = log2(pij/bi) * c
where bi is the background frequency of base i, and pij is the site-specific nucleotide frequency for nucleotide i at site j. c is a factor (constant) that we apply for convenience, by default c=100. If we assume a background frequency of 0.25 for each base, the sum (over i) of (pij/bi) is equal to 4.

FindM

Do you have a manual explaining how FindM works?

No, currently we don't have any user's manuals about FindM.

The program FindM scans a set of genomic sequences that are aligned relative to a given anchor point (TSSs, ChIP-seq peak centers, etc.) to find motif matches. Motifs are either defined by a consensus sequence or a position-specific scoring matrix (PWM). The result is a list of (best) motif matches. Output is provided in different formats: FPS which is the SSA-specific working format, SGA, and BED. The genomic positions represent motif matches.

We provide an on-line tutorial with details about SSA and FPS-dependent sequence retrieval mechanism:

The tutorial needs an update.

For more details on the SSA-specific FPS file format, please refer to the EPD user's manual:

Last update July 2017