Question: Can I submit my own sequences or genome coordinates to WebMOTIFS?
Answer: No. You can submit only gene or probe names. For every array or set of genes we add to WebMOTIFS, we do a set of calculations that lets us compare results from diffferent motif discovery programs.
(We are currently working on an options that will allow you to submit genome coordinates, to be used for analysis of ChIP-seq data. We will keep you updated on our progress.)
Question: Where can I find more information on the arrays included in WebMOTIFS?
Answer: Please see this page of array information.
Question: WebMOTIFS doesn't recognize my gene/probe names. What's wrong?
Answer: Please see this page with sample names to check that your gene/probe names are in the correct format. Please check that the version of the array you're using is the same as the one included in WebMOTIFS. And, if you're uploading a file of names, check that it's in the correct format (see the next question for details). If you're still stuck, email us.
Question: Can I upload a ".doc" file of gene/probe names?
Answer: No, you must upload a plain text (".txt") file, not a ".doc" or ".rtf" file. If WebMOTIFS is not recognizing your IDs, you may be uploading an incorrectly formatted file. Please try copying and pasting the IDs in the "Gene/probe name" text box.
Question: My motif of interest isn't included in THEME's initial hypotheses. What should I do?
Answer: You can download the command line version of THEME, from this website. This wiil allow you to use your own motifs as hypotheses.
If you have an initial hypothesis of general interest, email us and we'll consider adding it to WebMOTIF's list of initial hypotheses.
Question: I haven't gotten an email with my results yet. What should I do?
Answer: WebMOTIFS does a lot of computations, so your job may take up to 24 hours to complete. If you do not receive your results within 24 hours, please email us.
Question: How do you prioritize jobs?
Answer: WebMOTIFS processes jobs in the order received.
Question: How do you handle repeat ids?
Answer: A repeat ID will be treated the same way as a single ID (that is, only the first copy of the ID will be kept for analysis).
Question: Can you add a new array/new genome?
Answer: We regularly add new arrays to WebMOTIFS. Please email us with your request, and we'll let you know. Please note that it may take us several months to add a new array or genome (but we'll keep you updated on our progress).
Question: WebMOTIFS limits each user to 10 submissions a day, but I need to run more jobs. What should I do?
Answer: We have a command-line version of WebMOTIFS available, so you can run jobs on your own computer. (Note that this has not been extensively tested; please email us with any bugs.)
Question: Can I include expression fold changes?
Answer: No. WebMOTIFS currently does not allow you to associate numerical values with gene/probe names.