SNAP is a tool aimed at aiding researchers in the discovery and analysis of sequence motifs. Each user has his/her own account in which he/she can upload and save data, perform various analysis tasks , save the results on the server, or download them for further processing by related software.
Utilities of SNAP include:
- Ab initio motif search: Using the SeedSearcher software, one can discover sequence motifs which discriminates a subset of DNA sequences (such as a set of promoter sequence of genes suspected of being co regulated).
- Known motif search: The SeedSearcher software is able to upload known motifs, search for similar motifs and test measure the statistical significance of their over-representation in a subset of DNA sequences.
- Incorporate several sources of data to help direct the motifs search, when available:
- Prior belief about regulation (e.g results of ChIP experiments).
- Prior knowledge of positional bias or sequence conservation.
- Relate novel motifs to known regulatory motifs: SNAP has a built in tool to compare two PSSM motifs and estimate the pvalue that they are randomly similar. Any new motif can be compared to a local database of known motifs and to any other motif a user uploads into his account.
- Export results for further processing. This includes
- Motif refinement - for improved binding sites predictions etc. This is done by using the LearnMotif program to learn PSSMs or more generally Bayesian Network motifs. See how to export results to LearnMotif here.
- Relation to gene expression and various gene attributes: Motifs can be uploaded into the GeneXPress program. This enables the researcher to relate motifs to many other gene attributes and gene expression patterns. See how to export results to GeneXPress here.
- Upload motifs into the Genome Browser at UCSC