PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences
| Autor: | Miroslav Šulc, Ray M. Marín, Jiří Vaníček, Harlan Robins |
|---|---|
| Rok vydání: | 2015 |
| Předmět: |
False discovery rate
Untranslated region Genetics Internet Web server Messenger RNA Three prime untranslated region Biology computer.software_genre MicroRNAs Open Reading Frames Open reading frame microRNA Web Server issue RNA Messenger 3' Untranslated Regions computer Algorithms Software Coding (social sciences) |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets), which identifies primarily mRNA transcripts targeted in their 3′ untranslated regions (3′ UTRs), and (ii) PACCMIT-CDS, designed to find mRNAs targeted within their coding sequences (CDSs). While PACCMIT belongs among the accurate algorithms for predicting conserved microRNA targets in the 3′ UTRs, the main contribution of the web server is 2-fold: PACCMIT provides an accurate tool for predicting targets also of weakly conserved or non-conserved microRNAs, whereas PACCMIT-CDS addresses the lack of similar portals adapted specifically for targets in CDS. The web server asks the user for microRNAs and mRNAs to be analyzed, accesses the precomputed P-values for all microRNA–mRNA pairs from a database for all mRNAs and microRNAs in a given species, ranks the predicted microRNA–mRNA pairs, evaluates their significance according to the false discovery rate and finally displays the predictions in a tabular form. The results are also available for download in several standard formats. |
| Databáze: | OpenAIRE |
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