RASP Released

Sept. 13, 2020

RASP (RNA Alatas of Structure Probing) is a transcriptome-scale RNA structure probing database. Currently, RASP contains 161 deduplicated transcriptome-wide RNA secondary structure probing datasets from 38 papers. RASP covers 18 species across animals, plants, bacteria, fungi, and also viruses, and categorizes 18 experimental methods including DMS-Seq, SHAPE-Seq, SHAPE-MaP, and icSHAPE, etc. RASP also provides a user-friendly interface to query, browse, and visualize RNA structure profiles, offering a shortcut to accessing RNA secondary structures grounded in experimental data.

How to download data
1. In [Browse] page, users can highlight a region and click "save track data" to download a small amount of data;
2. In [Download] page, users can download GFF annotation file and fasta sequence file. Users can also choose criterions and download bigWig files. Users can convert the the bigWig binary file to bedGraph text file by bigWigToBedGraph tool.

How to retrieve a gene or sequence
1. In [Search] page, users can select a species and input the gene symbol, ensembl gene id or transcript id, then click the "Search" button. The server will return a page display the transcripts or genes. Users can click the "Go" button to browse the structure score in JBrowse (https://jbrowse.org/) or click a transcript to visualize the sequence and score;
2. In [Search] page, users select a species and provide a short sequence (no more than 200nt), then click the "Search Sequence" button. The server will use blastn  (https://www.ncbi.nlm.nih.gov/books/NBK279680/) command line tool to search the target genome sequence;
3. In [Browse] page, user can also search a gene symbol or provide a genome location.

Please jump to the [Help] page for more help information. Welcome to give us feedback (Pan Li: lip16@mails.tsinghua.edu.cn).


RASP: an atlas of transcriptome-wide RNA secondary structure probing data, Pan Li*, Xiaolin Zhou*, Kui Xu and Qiangfeng Cliff Zhang#, Nucleic Acids Research (In press)