About bpRNA-1m

bpRNA-1m consists of 102,318 RNA Secondary Structures from 7 differenet sources with their base pairing information[1]. For each RNA, we provide bpseq file, fasta file, dot bracket file, and structure type file. Moreover, the pdf file of each RNA secondary structure is available. All of the files and scripts are available to download from the download page.

The 7 data sources of bpRNA-1m are as follow:

   1. CRW: The Comparative RNA Web (CRW) Site [2]

   2. tmRNA: tmRNA Database [3]

   3. SRP: Signal Recognition Particle Database [4]

   4. SPR: Sprinzl tRNA Database (tRNAdb) [5]

   5. RNP: The RNase P Database [6]

   6. RFAM: The RNA Family Database [7]

   7. PDB: RCSB Protein Data Bank [8]





Version 1.0 - March 25th 2018

bpRNA-1m version 1.0 is the initialization of this metadatabase. This version contains all the data and information we have in the paper. There are 102,318 different RNA Structures exist in this version, all of which are single molecule. The base-pairing information as well as structure details are available to download.



Citation

1. Danaee P, Rouches M, Wiley M, Deng D, Huang L, Hendrix DA. bpRNA: Large-scale Automated Annotation and Analysis of RNA Secondary Structure. bioRxiv. 2018 Jan 1:271759.

2. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC bioinformatics. 2002 Dec;3(1):2.

3. Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J. tmRDB (tmRNA database). Nucleic acids research. 2003 Jan 1;31(1):446-7.

4. Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T. SRPDB: signal recognition particle database. Nucleic acids research. 2003 Jan 1;31(1):363-4.

5. Jühling F, Mörl M, Hartmann RK, Sprinzl M, Stadler PF, Pütz J. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic acids research. 2008 Oct 28;37(suppl_1):D159-62.

6. Brown JW. The ribonuclease P database. Nucleic acids research. 1998 Jan 1;26(1):351-2.

7. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic acids research. 2003 Jan 1;31(1):439-41.

8. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank, 1999–. InInternational Tables for Crystallography Volume F: Crystallography of biological macromolecules 2006 (pp. 675-684). Springer Netherlands.