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 rPredictorDB: the Why & the What.
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:
and much more. See the rPredictorDB record detail for a detailed description of information available from our database and CP-predict: a two-phase algorithm for rRNA structure prediction for details on the custom prediction algorithm.
The Biological background page will help you understand what’s going on here.
For unknown terminology, make sure you check out the rPredictorDB glossary.
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:
A complete description of the individual fields for search results is available here: rPredictorDB record detail.
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: CP-predict2
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.
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: Creating your own tool.
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.
Try the rWeb Tutorial and see if it’s still confusing afterwards. If it is, then ask us!
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.
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: Creating your own tool
You still need to tell us, though, to get developer access.
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: