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  1. Can I submit a sequence simply by telling the software the accession id of the gene I'm interested in?
  2. Can I submit sequences and evidence scores saved as a Word document?
  3. My sequence file is not being read in by the software.
  4. How should my file of evidence scores be formatted?
  5. My evidences file is not being read in by the server. What's wrong?
  6. How are the results of ProbTF reported?
  7. Can I use ProbTF with my own matrices that I have?
  8. How long will my results be saved on the server?
  9. Are sequences analyzed on both strands?
  10. How many TFs/matrices are there?

1. Can I submit a sequence simply by telling the software the accession id of the gene I'm interested in?

No. ProbTF is not connected to any sequence database and so does not 'understand' identifiers from say EntrezGene, RefSeq, EnsEMBL etc. Sequences to be analyzed must be input in FASTA format only.

This decision was made to avoid problems arising when trying to analyze genes with multiple translations. Questions over which sequence is the correct promoter become tricky to answer. Also, there are differing views as to whether UTR regions should be included in the analyses too. Rather than having to deal with these issues, the user determines exactly what sequence is scanned. Therefore, if an 'expected' site is not reported, then this may be due to the wrong sequence being scanned.

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2. Can I submit sequences saved as a Word document?

No. Sequences should be saved as simple text files. If you are using Word, use Save As to create a simple text file.

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3. My sequence file is not being read in by the software.

Check that you are not trying to submit a Word document or something with formatted text. ProbTF ONLY understands simple, text files.

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4. How should my file of evidence scores be formatted?

  • Each line in the file should contain a SINGLE probability/score value for each basepair in the matching sequence file.
  • The scores should range between 0 and 1 (value 1 is excluded). For cases where the evidence score is 1, these are set to 0.9999999.
  • The number of scores in the evidence file MUST match the same number of basepairs in the sequence file.
  • Note that depending on the type of your additional evidence, you may need to scale the probability scores closer to value 0.5, e.g. between 0.4 and 0.6. For example, we found that evolutionary conservation probabilities from PhastCons program produce the best results when they are scaled between 0.46 and 0.54.
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5. My evidences file is not being read in by the server. What's wrong?

  • The file should NOT be a Word document.
  • Each line in the file should contain a SINGLE score value for each basepair in the matching sequence file.
  • The scores should range between 0 and 1.
  • The number of scores in the evidence file MUST match the same number of basepairs in the sequence file.
  • And just to repeat, the file should NOT be a Word document.
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6. How are the results of ProbTF reported?

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7. Can I use ProbTF with my own matrices that I have?

At the current time, no. This is something that we may explore in the near future.

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8. How long will my results be saved on the server?

The raw results files remain on the server for a week before they are removed.

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9. Are sequences analyzed on both strands?

At the current time, no. This is something that we may add in the near future. In the meantime, you can analyze both strands of your sequence separately.

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10. How many TFs/matrices are there?

Mouse: 121 TFs and 187 motif models

For a full description of the motif model sets please see here.

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