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RBPmap - Motifs Analysis and Prediction of RNA Binding Proteins

In FASTA format (view example). Or genomic coordinates (view example). Paste your sequences/coordinates here:. Or, upload a file:. Search RBPmap motifs database: (To view the search results, the browser's pop-up blocking should be turned off). Enter an RNA binding protein name, symbol or common alias:. Or, Click here. To select motifs from RBPmap full list. Choose your own motifs (optional):. Enter a consensus motif (4-10 bp long, IUPAC symbols only). Upload a probability matrix file ( in MEME format.

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RBPmap - Motifs Analysis and Prediction of RNA Binding Proteins | rbpmap.technion.ac.il Reviews

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In FASTA format (view example). Or genomic coordinates (view example). Paste your sequences/coordinates here:. Or, upload a file:. Search RBPmap motifs database: (To view the search results, the browser's pop-up blocking should be turned off). Enter an RNA binding protein name, symbol or common alias:. Or, Click here. To select motifs from RBPmap full list. Choose your own motifs (optional):. Enter a consensus motif (4-10 bp long, IUPAC symbols only). Upload a probability matrix file ( in MEME format.

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1 overview

2 manual

3 versions

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6 genome

7 human

8 mouse

9 d melanogaster

10 database assembly

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RBPmap - Motifs Analysis and Prediction of RNA Binding Proteins | rbpmap.technion.ac.il Reviews

https://rbpmap.technion.ac.il

In FASTA format (view example). Or genomic coordinates (view example). Paste your sequences/coordinates here:. Or, upload a file:. Search RBPmap motifs database: (To view the search results, the browser's pop-up blocking should be turned off). Enter an RNA binding protein name, symbol or common alias:. Or, Click here. To select motifs from RBPmap full list. Choose your own motifs (optional):. Enter a consensus motif (4-10 bp long, IUPAC symbols only). Upload a probability matrix file ( in MEME format.

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rbpmap.technion.ac.il

1

RBPmap - Motifs Analysis and Prediction of RNA Binding Proteins

http://rbpmap.technion.ac.il/index.html

In FASTA format (view example). Or genomic coordinates (view example). Paste your sequences/coordinates here:. Or, upload a file:. Search RBPmap motifs database: (To view the search results, the browser's pop-up blocking should be turned off). Enter an RNA binding protein name, symbol or common alias:. Or, Click here. To select motifs from RBPmap full list. Choose your own motifs (optional):. Enter a consensus motif (4-10 bp long, IUPAC symbols only). Upload a probability matrix file ( in MEME format.

2

RBPmap - Motifs Analysis and Prediction of RNA Binding Proteins

http://rbpmap.technion.ac.il/overview.html

RBPmap is a computational tool that enables accurate prediction and mapping of RNA binding proteins (RBPs) binding sites on any RNA sequence or list of sequences of interest, provided by the users (as either sequences or genomic coordinates). RBPmap has been developed specifically for mapping RBPs in human, mouse and drosophila melanogaster genomes, though it supports mapping RBP binding sites in other organisms too. A detailed description of RBPmap algorithm:. Calculating a match score for the motif.

3

RBPmap - Motifs Analysis and Prediction of RNA Binding Proteins

http://rbpmap.technion.ac.il/manual.html

Genome and Database Assembly:. RBPmap enables full functionality for the following genomes:. December 2013 (GRCh38/hg38) assembly. Provided by the Genome Reference Consortium. February 2009 (GRCh37/hg19) assembly. Provided by the Genome Reference Consortium. March 2006 (NCBI36/hg18) assembly. Provided by the International Human Genome Sequencing Consortium. December 2011 (GRCm38/mm10) assembly. Provided by the Mouse Genome Reference Consortium. July 2007 (NCBI37/mm10) assembly. The user can select the mo...

4

RBPmap Motifs Selection

http://rbpmap.technion.ac.il/RBPmap_motif_selection.html

Search the following list and select the proteins/motifs of interest. Check/uncheck a protein name in order to select/deselect all its ascribed motifs). Human / Mouse motifs. PMID: 23846655, PMID: 22574288. PMID: 23846655, PMID: 22574288. PMID: 19296853, PMID: 22574288. PMID: 23846655, PMID: 19124611. PMID: 19296853, PMID: 17942744. PMID: 19561594, PMID: 19296853. PMID: 10094314, PMID: 19296853. PMID: 10094314, PMID: 19296853. PMID: 23846655, PMID: 17548433. PMID: 11222770, PMID: 19296853.

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RBPmap - Motifs Analysis and Prediction of RNA Binding Proteins

http://rbpmap.technion.ac.il/download.html

Download a stand-alone version of RBPmap. Disk space: 20-30Gb (Depends on the number of genomes). Perl (including the following special modules: DBI. MySQL server ( http:/ dev.mysql.com/doc/refman/5.7/en/linux-installation.html. Download the following files:. Including RBPmap scripts and UCSC files and utilities). RBPmap MySQL dump file. Installation and configuration of RBPmap package:. A sub-directory named 'RBP PSSMs' which contains the PSSM motifs stored in RBPmap database (a file per each motif).

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yaelab.technion.ac.il

Mandel-Gutfreund Lab | Tools

http://yaelab.technion.ac.il/tools.html

RBPmap: a web server for mapping binding sites of RNA-binding proteins. Paz et al., Nucleic Acids Res., 2014. DRIMust: a web server for Discovering Rank Imbalanced Motifs Using Suffix Trees. Leibovich et al., Nucleic Acids Res., 2013. SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Paz et al., Nucleic Acids Res., 2010. NAbind: classifying NA-binding proteins based on electrostatic properties. Shazman et al., PLoS CB., 2008.

sfmap.technion.ac.il

SFmap - Motifs Analysis and Prediction of Splicing Factors

http://sfmap.technion.ac.il/index.html

We highly recommend to use our upgraded RBPmap. Web-server (including SFmap features and more) instead of SFmap. Human Feb. 2009 (hg19). Human Mar. 2006 (hg18). Sequence (In FASTA format). (View example). Genomic coordinates ( chromosome:start-end:strand. Paste your sequences/coordinates here:. Sequence length: 21-5,000 bp; Max. number of entries: 5,000). Note that the input size limitations have changed in version 1.8. Or, upload a file:. Motifs selection (optional, default: all motifs).

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rbpmap.technion.ac.il

RBPmap - Motifs Analysis and Prediction of RNA Binding Proteins

In FASTA format (view example). Or genomic coordinates (view example). Paste your sequences/coordinates here:. Or, upload a file:. Search RBPmap motifs database: (To view the search results, the browser's pop-up blocking should be turned off). Enter an RNA binding protein name, symbol or common alias:. Or, Click here. To select motifs from RBPmap full list. Choose your own motifs (optional):. Enter a consensus motif (4-10 bp long, IUPAC symbols only). Upload a probability matrix file ( in MEME format.

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