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Return to UTRome home
Frequently Asked Questions.
[What is the UTRome?]
[Why should I use it?]
[But if all these data are already available in other databases, why should I use the UTRome?]
[What kind of tools are available?]
[Why does my query return multiple results with similar names?]
[Why is my gene of interest is not available?]
[I cannot display the trace file!]
[I do not understand the C.Brigssae alignment in the pictogram.]
[What do the colours in the unafold prectiction mean?]
[There is a specific clone/transcript that I really want/need. How can I get it from you?]
[How can I help to improve the annotation in the UTRome?]
Question #1.
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Question 1: What is the UTRome?
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A: The UTRome is a comprehensive resource for 3'UTR biology in C.elegans. The database provides detailed information on the 3'UTR of every transcribed C.elegans mRNA using data extracted from other databases such as WormBase, PicTar and others. In addition, as part of the ModENCODE Consortium, we developed a high-throughput cloning pipeline that produces wet-bench validated 3'UTR sequences, which will be continuously deposited into the database.
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Question #2
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Question 2: Why should I use it?
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A: This database has been developed specifically for 3'UTR biology. If you are interested in 3'UTRs you will find this website very informative.
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Question #3
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Question 3: But if all these data are already available in other databases, why should I use the UTRome?
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A: Even though some of the data present in this database is already available elsewhere, we simplified the search process for the user by filtering and pre-processing the data. In addition, we compare these data with the output of our cloning pipeline. Our data provide validation and, in some cases, evidence of the existence of new 3'UTRs. Therefore, we hope to provide the user with the most complete set of data available for 3'UTR biology in C.elegans in a single, user-friendly website.
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Question #4
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Question 4: What kind of tools are available?
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A: At this stage we are providing a limited set of tools since our cloning pipeline is not complete yet. 1) Batch Download extracts 3'UTR sequences both from our cloning pipeline and from your gene of interest. 2) Trace File Viewer is an applet to visualize raw ABI Trace Files from our cloning pipeline.
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Question #5
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Question 5: Why does my query return multiple results with similar names?
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A: Every search returns both the annotated transcripts from WormBase and the transcripts present in our cloning pipeline. To differentiate them, we tag our UTRs with an .mm just after the transcript name (e.g. D2045.6 vs D2045.6mm). If we designed multiple primers for a given UTR, we numbered the extension (.mm1, .mm2 etc)..
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Question #6
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Question 6: Why is my gene of interest is not available?
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A: Work on our cloning pipeline is still ongoing and we are continuously releasing new data. Please come back and check the website over the next few months and you may be able to find it then. If you need help with a specific transcript, which is not available in our cloning pipeline, feel free to contact us and let us know.
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Question #7
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Question 7: I cannot display the trace file!
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A: You are most probably using Microsoft Explorers family of browser. Microsoft never fully supported the JAVA standard set by its creator SUN Microsystem. As result, you may experience problems if you want to see the trace file using our Java Applet. We are aware of freezing, blank screens and popup alerts that prevent the application from running. The best solution is to download the original JAVA toolkit from Suns website.
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Question #8
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Question 8: I do not understand the C.Brigssae alignment in the pictogram.
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A: The track is colored in blue and the intensity of the color marks the quality of the alignment. If present, multiple contigs are displayed. For more information please look at the WormBase tutorial.
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Question #9
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Question 9: What do the colours in the unafold prediction mean?
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A: The Mfold algorithm predicts suboptimal folding for a given RNA sequence. According to the Mfold manual, the color annotation indicates the propensity of individual nucleotides to participate in base pairing and whether or not a predicted base pair is 'well-determined'. The scale ranges from well determined to poorly determined following Red->Yellow->Green->Blue->Purple->Black. Please see this image or go to the mfold manual for more information.'
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Question #10
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Question 10: There is a specific clone/transcript that I really want/need. How can I get it from you?
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A: As soon as our data is released, you are more than welcome to contact us with specific requests. We are currently working to distribute our clones through well-established distributors.
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Question #11
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Question 11: How can I help to improve the annotation in the UTRome?
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A: In the 'Cloning' page we have inserted a table containing a web-form named 'Feedback'. Users who note inaccuracies in our curation can use this form to suggest new cis-acting motifs and other important features we may have improperly annotated or that are missing.
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