What are miRNAs?
MicroRNAs (miRNAs) are a class of single-stranded RNAs that are widely evolutionary conserved among many known species. These short (18-24 nt), non-coding molecules mediate post-transcriptional gene expression regulation by promoting cleavage or inhibiting translation of the target mRNA. By described interaction miRNA play various important roles in living organisms.
What is tools4miRs?
Tools4miRs is a first, manually-curated platform gathering large amount of methods for the broadly-defined miRNA analysis. Tools4miRs is also a web-based target prediction meta-server incorporating user-designated methods in the analysis of user-provided data.
Who can use tools4miRs?
Anyone – Tools4miRs is user-friendly and open-access service. No registration is needed to exploit its full functionality.
What information can I get from each tools4miRs section?
All tools in the tools4miRs are categorized into four general and seven more detailed sections. General: 1) Databases - includes wide range of miRNA-related data collections, such as miRNA sequences, experimentally validated targets, predicted targets, miRNA expression level in different cells/tissues/conditions, targets expression level, disease associations and several others. 2) Sequencing Data Analysis - stores methods specifically dedicated to the examination of high-throughput sequencing data (e. g. sRNA-Seq, RNA-Seq, PARE and CLIP-Seq) generated from different sequencing platforms. Mentioned tools provides specific analysis concerning features like: novel and known miRNA identification, target prediction and annotation or differential expression investigation. 3) All-In-One Tools – this section is similar to one described above, but instead of focusing the analysis on specific features (e.g. known miRNA identification and differential expression) they provide complex analysis of high-throughput sequencing data. 4) Other tools - includes methods which are interesting and relevant from the miRNA-analysis point of view; however, basing on their main scope they could not be classified in any of available general or detailed categories. Specific software – tools from these categories may or may not require (as an input) high-throughput sequencing data: 1) Novel miRNA / Precursor Analysis – computational approaches gathered here focus on the novel miRNA molecules identification or distinguishing real miRNA precursors from the pseudo pre-miRNA. Analyses performed by these tools are based on divergent algorithms and consider specific features such as structure, sequence and conservation. 2) Target Prediction – stores bioinformatics methods designed for identification of potential miRNA binding sites in a target sequence. The aforementioned tools incorporate several common (seed match, conservation, free energy or site-accessibility) and less common (target-site abundance, local AU content or 3' compensatory pairing) features on which miRNA target prediction is based. 3) Target Functional Annotation – useful tools enabling user to perform functional analysis of given miRNA targets. This may include: GO (Gene Ontology) and DO (Disease Ontology) term annotation/enrichment examination, metabolic KEGG pathway analysis, expression correlation between miRNA and their targets, literature mining and others. 4) miRNA-SNP analysis – includes methods which examine influence of single nucleotide polymorphisms (SNP) on miRNAs and their interaction with potential targets. Some tools from this section may require already predicted targets for given miRNAs. 5) Known miRNA identification – gathers bioinformatics approaches designed to search for known miRNAs in provided data sets (in most cases these are deep sequencing data) 6) isomiRs identification – tools useful for identification of isomiRs, that is molecules having variations in sequence length/composition with respect to reference, known miRNA. Described type of methods requires (usually) results of sRNA deep sequencing data. 7) Differential Expression Analysis – stores computational approaches which evaluate miRNA or their targets expression differences between given sets. These tools can be based on known differential expression algorithms, such as edgeR or DESeq2.
How can I filter tools available in tools4miRs tables?
Filtering tools in tools4miRs is very simple: 1) Go to appropriate tool section from main menu. 2) On „Filter Panel” choose appropriate criteria according to your preferences and needs. If you have any doubts concerning the meaning of a given field - please point your cursor on it or on the help icon to get an additional hint/instruction. 3) Click „Filter” - table with tools will automatically refresh. 4) To remove filtering and see table with all tools gathered in this section – click „Clear Filtering”.
How should I interprate fileds in „Organism Specific” section available in the Filter Panels?
„Organism Specific” section is divided into three subsections depending on the level of specificity: any organism (2), specific specie (1) or kingdom/subgroup of it (3). Selection between these three subsections will return the result of logical operator „OR”, while criteria selection within one subsection will return the result of logical operator „AND”. Example 1: selected – plants, human results- tools dedicated to analyze plants OR human data. Example 2: selected – human, mouse results – tools dedicated to analyze human AND mouse data.
Can I get more information about tools than those seen in table?
Yes – clicking on the tools name leads to its extensive description, where you can find information concerning: algorithm, ease of use/installation, performance, cross-references, adjustability, license, publication citation, last software update, analysis schemes and several others.
How can I go to the Target Prediction Meta-Server ?
Target Prediction Meta-Server can be accessed in two different ways – via „Target Prediction Server” menu or by „Target Prediction” menu after switching „Browse” to „Analyse” mode.
How to predict miRNA targets using tools4miRs Target Prediction Meta-Server?
Please follow these steps: I) Go to "Target Prediction Server" menu or "Target Prediction" menu and switch from "Browse" to "Analyse" mode. II) Select methods you would like to use for you miRNA targets analysis. If you would like to previously filter available target prediction methods, please use the "Filter Panel". III) Upload your mRNA and miRNA sequences (in FASTA format). Set the parameters of chosen methods or leave it as default. Optionally, you can provide your email address (for further obtaining the results), calculations job title and description. IV) Start the analysis. V) After all calculations are finished; the results will be displayed in table form.
In what format should I paste/upload sequences for the target prediction analysis?
Target Prediction Meta-Server accepts only sequences in the FASTA format.
Are there any limits for uploaded miRNA/mRNA sequences?
Yes, there are limits – in case of miRNA the provided FASTA file should contain no more than 500 sequences of length between 6 and 28, while for mRNA file there should be no more than 10000 sequences of length between 30 and 20000 nucleotides.
How long my target prediction computation will take?
It depends on number of miRNA/mRNA sequences you uploaded and target prediction method you selected. Please be aware that in case of some target prediction methods calculating the results may take a while. After target prediction job submission you will see statuses (Waiting, Running, Finished) for each selected tool separately, so you are up-to-date with your analysis progress.
What is the difference between the Basic and Extended view mode of the target prediction results?
In the Basic view the results are grouped by unique miRNA:target pairs, which are shown together with the number of target binding sites, the check marks of appropriate tool names and total tools number that predicted given pair. The Extended form shows results grouped by individual/unique binding site of miRNA-mRNA. Therefore, the exact "from:to" position and total tools number that predicted specific site is provided. Moreover, the information about score, binding energy or other validation value calculated by chosen method are given as well. Please see "Sample Results": http://tools4mirs.org/prediction/status/eee0dfe6-ec40-48ae-9c0f-1bae4cd49fed/
Can I select "Union" or "Intersection of my chosen methods?
Yes - after the target prediction table is generated you may chose the "Union", "Intersection" or "Consensus" of selected methods and do the post-processing of the obtained results. The "Union" of given tools should be interpreted as result, which minimum one method predicted specific target. The "Intersection" results in only those targets predicted by all computational approaches used. While, "Union" provides information concerning specific target predicted by X out of all Y methods used (e. g. 4 out of all 5 methods used).
Why number of results from the same analysis differ when choosing "Intersection" the Basic and "Intersection" in the Extended mode?
Basic and Extended are two different analysis modes. Basic mode denotes unique pairs of mRNA and miRNA, while Extended mode treats triplets (miRNA, mRNA, and position in given mRNA) unique. In this case, when you additionally choose to obtain for example Intersection of your results, the overall number of results from Extended mode will be different than from Basic because the server will return only those results = exact same target positions which are predicted by all used methods. In Basic mode the result will represent same miRNA:target pair predicted by selected methods.
Can I additionally filter the obtained target prediction results?
Yes - after generation of the result table, you are able additionally to sort and filter obtained data by dismissing/forcing to display results predicted by selected method. Additionally, you can search through the result table.
Can I obtain my target prediction results by email?
Yes – during the submission of new target prediction job you can provide your email address. After the calculations are finished you will received email confirmation with URL link to your target prediction results.
Can I download the calculted target prediction results?
Yes - you can download all your results (even filtered or sorted) in CSV, XLS and XLSX format. Additionally you are able to download the original results from each of target prediction methods used, as well as miRNA/mRNA sequences provided as an input for the target prediction meta-server.
Can I go back to my results at any time? For how long my results will be available?
Partly Yes - if you keep the URL link to your target prediction results you can go back to them any time during the 30 day period (starting from the date of finishing your target prediction job). After that time your target prediction result will be removed form the server. If you would like to get a reminder with the URL links to your previosu jobs please use „My Jobs” form and provide your e-mail address that you have used during jobs submissions.
Can I submit new tools?
Yes – to submit new tool please go to the „Submit Tool” section from main menu and fill in the form (required fields are minimum). After data validation, we will incorporate submitted tool into tools4miRs.
What types of tool can I submit?
You can submit any tool which falls in one of the listed 4 general and 7 more detailed categories. To maintain the quality of collected tools we accept only methods which are already published.
After submitting a tool I realized that I have made a mistake – what should I do?
In this situation, please contact us using the „Contact” form from main menu.
Can I suggest a new tool category?
Yes, of course – we are open for any suggestions and comments. Please feel free to contact us using the „Contact” form.
Can I add a comment to a specific tool?
Yes - you can add coment to every tool from tools4miRs and rate it as well. Just click on the given tool name, which will lead you to it's extansive description and then go to the end of the page where you will find "Comments & Rating" field.