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Created on: 04-Mar-2014   Last updated on: 04-Mar-2014 |  How to cite this?
A compilation of piRNA resources
Sirisha N. and Swetha Cheena (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources

Important features / utilities*CitationsYear of publicationRank by usage frequency Add comments
RNAdb 2.0
http://research.imb.uq.edu.au/rnadb/
Sequences of dirfferent pirna can be downloaded
Pang, KC, Stephen, S, Dinger, ME, Engstrom, PG, Lenhard, B, Mattick, JS (2007).RNAdb 2.0--an expanded database of mammalian non-coding RNA.Nucleic Acids Res 35: D178-182. PMCID: PMC1751534.PMID:17145715
2007
10
piRNABank
http://pirnabank.ibab.ac.in/
It compiles all the possible piRNA clusters and gives the information of piRNA information for the gene and also for the genomic repeat elements
piRNABank: a web resource on classified and clustered Piwi-interacting RNAs". Sai Lakshmi S, Shipra Agrawal.Nucleic Acids Research 2008 January; 36 (Database issue): D173 D177. [PMCID: PMC2238943]. PMID:17881367
2008
26
frnadb
http://www.ncrna.org/frnadb/
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K.Nucleic Acids Res. 2007 Jan;35(Database issue):D145-8. Epub 2006 Nov 11.PMCID: PMC1669753. PMID:17099231
2007
35
deep base
http://deepbase.sysu.edu.cn/index.php
It is used for annotating and discovering small and long non coding rna from next generation sequencing data
Jian-Hua Yang, Peng Shao, Hui Zhou, Yue-Qin Chen, and Liang-Hu Qu.deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 2010 Jan;38(Database issue):D123-D130. Epub 2009 Dec 4. PMID: 22144203
2010
50
NONCODE
http://www.noncode.org/
It gives information about the noncoding RNA and the sequences are confirmed manually using references.More than 80% of data is from the experimental data
NONCODE v2.0: decoding the non-coding.Nucleic Acids Research, 2008 , Vol. 36, Database issue D170-D172.PMCID:PMC2238973 PMID: 18000000
2008
64
ncRNAimprint
http://rnaqueen.sysu.edu.cn/ncRNAimprint/
ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs. Zhang Y, GuanDG, Yang JH,Shao P,Zhou H,Qu RNA. 2010 Oct;16(10):1889-901. doi: 10.1261/rna.2226910. Epub 2010 Aug 26.
2010
87
piRNA predictor
http://59.79.168.90/piRNA/index.php
Used to predict pirna from the given sequences
A k-mer scheme to predict piRNAs and characterize locust piRNAs.Zhang Y, Wang X, Kang L. Bioinformatics. 2011 Mar 15;27(6):771-6. doi: 10.1093/bioinformatics/btr016. Epub 2011 Jan 11. PMCID: PMC3051322 PMID:21224287
2011
95
BlastR
http://www.tcoffee.org/Projects/blastr/
Used to find homologous ncrna by searching in databases
BlastR--fast and accurate database searches for non-coding RNAs. Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C. Nucleic Acids Res. 2011 May 30. PMCID: PMC3167602. PMID: 21624887
2011
96
pirna cluster
http://www.uni-mainz.de/FB/Biologie/Anthropologie/492_ENG_HTML.php
It can be used to download datasets for pirna clusters for different species (human,macaque,mouse,rat)
Rosenkranz D, Zischler H. proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis. BMC Bioinformatics 2012, 13:5 doi:10.1186/1471-2105-13-5.PMCID:PMC3293768. PMID: 22233380
2012
100
pseudomap
http://pseudomap.mbc.nctu.edu.tw/php/
It is used to find TPG(Transcribed pseudogene) derived siRNA target interactions
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes. Wen-Ling Chan, Wen-Kuang Yang, Hsien-Da Huang and Jan-Gowth Chang. Database (Oxford). 2013 Feb 8;2013:bat001. doi:10.1093/database/bat001.PMCID:PMC3567485. PMID: 23396300
2013
100
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