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  1. Can I submit sequences to scan simply by telling the software the accession id of the genes I'm interested in?
  2. Can I submit sequences saved as a Word document?
  3. My sequence file is not being read in by the software?
  4. Are sequences scanned for repeats before they are analysed?
  5. How are the results of the scans reported?
  6. What is GFF format?
  7. Can I view my results using other software?
  8. Using the most stringent scans cut-off, I get no results?
  9. When I run my sequences I get a lot of hits. How can I reduce them?
  10. Do I need to change any of the parameter values for the individual algorithms to get them to run?
  11. The results in the PDF file are difficult to see as they are so dense?
  12. In Argo, why do the arrows for the predictions point in two different directions?
  13. The results in the Argo browser are mixed up. How do I create a clearer picture?
  14. Can I scan using my own matrices that I have?
  15. How long will my results be saved on the server?
  16. The Argo display does not work for me. What is Java Web Start and where do I get it from?
  17. Are promoter sequences scanned on both strands?
  18. I get an error message when trying to run Clover with sequences of greater than 5K basepairs. Why?
  19. What's different about the stringent matrices?
  20. How many matrices are there per set?
  21. What does Mogul stand for? Is it an acronym?

1. Can I submit sequences to scan simply by telling the software the accession id of the genes I'm interested in?

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

This decision was made to avoid problems arising when trying to scan 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 and is not the fault of the software.

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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. MotifMogul ONLY understands simple, text files .

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4. Are sequences scanned for repeats before they are analysed?

No. The algorithms should however run with masked sequences.

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5. How are the results of the scans reported?

Results are reported in 3 ways. [Back to top of page]

6. What is GFF format?

GFF stands for General Feature Format and is designed to report genomic features in a standard way. Amongst other data, it saves key details such as start and end coordinates of features and the scores assigned to them (if applicable). The full specification can be read here.

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7. Can I view my results using other software?

One reason for choosing GFF as the format in which to report results, is that it is a format that can be read by a number of genomic visualisation tools. Below is a list of other standalone software tools that read and display GFF files. Hence, if you wanted to download the raw GFF file from a set of scans and change the colours, number of scan tracks, etc., then a standalone package may be the way to go. We do not promote any one particular tool here, but in-house at the ISB we have found that Argo and Apollo have worked well for our needs.

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8. Using the most stringent scans cut-off, I get no results?

This is entirely possible as the most stringent cut-off is quite severe - selecting only the top 0.01% of predictions for a matrix's scores compared to random. Try using a lower stringency threshold.

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9. When I run my sequences I get a lot of hits. How can I reduce them?

Try selecting a more stringent cut-off threshold and/or adapting the parameters of the individual matrix scanning algorithms. For example, increasing the value of MotifLocator's Motif Threshold parameter value.

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10. Do I need to change any of the parameter values for the individual algorithms to get them to run?

No. The parameter values that initially appear in the windows are the default values that the algorithms run with out-of-the-box.

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11. The results in the PDF file are difficult to see as they are so dense?

The PDF visualisation of results is only intended to be a quick-and-easy way to view the results. It works well when there around 20-30 predictions. For only single hits, one tends to get large single blocks with large text. With tens to hundreds of hits, the display becomes too complex to read. Trying to find some middle-ground is difficult!!

If your results are too complex to interpret in PDF, try running scans one analysis at a time and view each of the individual PDFs separately. Or look at the results in Argo (or some other standalone GFF display tool) where you are able to interactively change the way the results are displayed.

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13. In Argo, why do the arrows for the predictions point in two different directions?

Arrows pointing to the right of the screen, indicate matrix hits predicted on the forward strand of the sequence. Arrows pointing to the left, are predictions on the reverse strand.

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14. The results in the Argo browser are mixed up. How do I create a clearer picture?

In a blank area of the sequence display window, right click on your mouse button to bring up an on-screen menu. Select the Track Table.. item. In the new menu that appears, in the Stack column, change the option for each track from Integrated to Segregated. This then separates the results into their own individual tracks.

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15. Can I scan using my own matrices that I have?

At the current time, no. This is something that we may explore in the near future for use with the individual scanning algorithms.

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

The raw GFF files remain on the server for a week before they are removed. PDF and Argo specific files are removed daily as they can accumulate very rapidly.

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17. The Argo display does not work for me. What is Java Web Start and where do I get it from?

Java Web Start is a software technology from Sun that allows applications to be launched on an end-users desktop machine, using any standard web browser. If it isn't installed on your machine, here's a simple tutorial guiding you through installation. And this is a more detailed one.

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18. Are promoter sequences scanned on both strands?

Yes. In the GFF file, a prediction on the forward strand is represented as a +. Predictions on the reverse strand are represented as a -.

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19. I get an error message when trying to run Clover with sequences of greater than 5K basepairs. Why?

To assess the significance of predictions Clover uses a set of background sequences as a reference set. This set of sequences must be at least as long as the promoter sequence(s) being analysed. This then becomes a trade-off between the maximum length of sequence to analyse and the time that it takes Clover to run: the longer the promoter sequence the longer the run time. The maximum sequence is set to 5K.

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20. What's different about the stringent matrices?

Stringent matrices are derived from a hand-curated list of matrices used in the paper. These are a subset of all the matrices on a species basis.

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21. How many matrices are there per set?

For a full description of the matrix sets please see here.

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22. What does Mogul stand for? Is it an acronym?

Mogul is gaelic for the mesh of a net. It is not an acronym.

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