.. _User-FAQ: Frequently Asked Questions ************************** .. _User-FAQ-general: rPredictorDB - general ==================== What is rRpredictor? -------------------- rPredictorDB is a bioinformatical infrastructure designed to make life easier for people who work with ribosomal RNA. These webpages are the public front-end of the infrastructure. For a more thorough description, see :ref:`User-index-why`. What can rPredictorDB do? ----------------------- We offer two general functionalities: searching in our large database of ribosomal RNA and predicting secondary structure of (mostly ribosomal) RNA. More specifically, we can for example: * find and retrieve rRNA molecules similar to molecules you give us, * compute detailed statistics about the secondary structures predicted for a sequence, * predict secondary structure for your rRNA sequences with an algorithm developed specifically with respect to ribosomal RNA and much more. See the :ref:`User-detail` for a detailed description of information available from our database and :ref:`User-cp-predict` for details on the custom prediction algorithm. That's nice, but I don't understand what it means! -------------------------------------------------- The :ref:`User-biology` page will help you understand what's going on here. For unknown terminology, make sure you check out the :ref:`User-glossary`. What kind of information can I find on rPredictorDB? -------------------------------------------------- We integrate data and information from the `SILVA `_, `Rfam `_ and `Taxonomy `_ (NCBI) databases and the `European Nucleotide Archive `_ and add structural data. The records in our database have several sections. For each record, we provide: * Information about sequence origin: unique ID of source molecule, organism name, taxonomy, etc. * Information about sequence itself: length, the actual sequence, various quality indicators * Predicted secondary structures, an analysis of structural features and a visualisation of the predicted structure * References to relevant scientific literature * Cross-references to other databases containing the same sequence * Additional annotations from the source databases A complete description of the individual fields for search results is available here: :ref:`User-detail`. How can I run your prediction algorithm on my data? ---------------------------------------------------- Have a look at the `rPredictorDB Predict page `_. rPredictorDB's custom algorithm is ``Cp-predict v.2``. A detailed description of the input fields is available here: :ref:`User-toolkit-reference-cppredict` There are many similar sites. Why should I use rPredictorDB? ---------------------------------------------------------- While there are several directly to ribosomal RNA, we (the `Bioinformatics laboratory of the Microbiological Institute of the Czech Academy of Sciences `_ and our team at the Faculty of Mathematics and Physics at Charles University) feel that a better job could have been done. The main drawbacks of similar bioinformatical websites are a sharp learning curve and missing information or unclear *purpose* of information. In order to use a website such as the `Protein Data bank `_ or the `Comparative RNA website `_, a user first has to have - or obtain - a good general idea of what the site does, why would anyone want such a site and what a *lot* of terminology means. After this background knowledge is obtained, a user finds out that certain information is not well-curated or made explicit: no one (at least publicly) keeps track of whether a RNA sequence was obtained directly of from a DNA transcription site, information about the type of rRNA is sparse, sometimes the phylogeny of a molecule is missing, a resolved secondary structure is not sufficiently labeled, it is unclear what constitutes a truly unique identifier of an RNA sequence or structure, etc. For instance, the `STRAND database `_ of resolved RNA secondary structures contains a number of structures inconsistently labeled for RNA-protein complexes and duplicate sequences. Another deficiency of such sites is often little or missing support for mass data retrieval. When present, it is usually in the form of pre-packaged archives and the user has little choice over what subset of the data to download. (A notable exception here is the `SILVA database `_ of rRNA molecules.) While perhap such drawbacks are of less concern to biologists, the fast-growing field of bioinformatics is sensitive to this kind of volatility in data sources. Nobody wants to spend a lot of time by finding out what uniquely identifies an RNA sequence or structure, filling in missing fields, etc., let alone downloading a set of several hundred sequences of interest one by one. rPredictorDB was designed with overcoming these drawbacks in mind. Our goal is first and foremost clarity: answers to questions such as "Why would I ever want to do that?" should be easy to find (and relatively easy to read). Also, we may randomly decide to give you a cookie. I have a great program you should use! -------------------------------------- You can go right ahead and write a rPredictorDB tool for your program. It's not hard! rPredictorDB was designed with extensibility in mind. How to write a tool is described here: :ref:`Technical-extending`. If you don't feel like coding but still want to contribute your program, `contact us `_ and if you convince us your program is worth it - which might not be so hard -, we'll implement the tool ourselves. .. _User-FAQ-site: Site usage ========== It's confusing: too many buttons! --------------------------------- Try the :ref:`User-rWebTutorial` and see if it's still confusing afterwards. If it is, then `ask us! `_ X isn't working! ---------------- `Tell us! `_ Make sure you describe your problem so that we exactly follow your steps to reconstruct it. If a screen with a large red strip at the top comes up and shouts about some kind of error, send us a screenshot! (Actually, you can send us a screenshot of the error anyway, it will nearly always help.) We'll get in touch. Doing Y should be possible. --------------------------- `Tell us! `_ We'll get in touch and discuss the functionality with you. If Y is a tool, you can also become an rPredictorDB developer and implement it yourself, according to your dreams and wishes - extending rPredictorDB with new tools is quite simple. (One of the key design concerns of rPredictorDB was extensibility.) Here's how to do it: :ref:`Technical-extending` You still need to tell us, though, to get developer access. .. _User-FAQ-can-I-help: Can I help? ----------- Of course! You can best start by `telling us about it `_, because nearly all ways of helping require access to the rPredictorDB development repository. You can contribute in many ways. Some ideas, from less to more technical: * Feedback. We appreciate any and all feedback. By telling us what you like or don't like about rPredictorDB, you help us make it better and thus help yourself to a better service. * Biological expertise. If you stumble across anything that's incomplete, imprecise or unclear, we'll be more than happy if you can help us clarify it. * The :ref:`glossary` always needs more terms, better formulations, etc. * Testing. This is a step up from feedback: you can participate in the bug hunt. Weird corner cases for input parameters, pointless tool combinations - the gloves are off. (Just please inform us *before* you bring the server down.) Testing rPredictorDB means detailed feedback: what exactly you did, whether it worked or not. If you wish to test, `contact us `_ and we'll point you to parts of rPredictorDB that need tester attention. * Tool development - the more, the merrier (within reason). Extensibility is one of the key design concern in rPredictorDB. Here's how to do it: :ref:`Technical-extending`