RIblast is ultrafast RNA-RNA interaction prediction software based on seed-and-extension algorithm for comprehensive lncRNA interactome analysis.
Version 1.2.0 (2019/11/02)
We used BL* energy model as RNA secondary structure energy model. You can download this energy model from http://www.cs.ubc.ca/labs/beta/Projects/RNA-Params We thank Dr. Mirela Andronescu for the development of this model.
RIblast consists of database construction search step and rna interactin search step. Firstly, you have to generate formatted database files from FASTA fomatted RNA sequences file using RIblast "db" command. RIblast "db" command requires 2 options ([-i InputFastaFile] and [-o OutputDbName]). Then, you can search RNA-RNA interaction of a query seuence to database sequences using RIblast "ris" command. RIblast "ris" command requires 3 options ([-i InputFastaFile], [-o OutputFileName] and [-d DatabaseFileName]).
./RIblast db -i dbRNA.fa -o test_db ./RIblast ris -i queryRNA.fa -o output.txt -d test_db
Command and Options
db: convert a FASTA file to RIblast database files RIblast db [-i InputFastaFile] [-o OutputDbName] [-r RepeatMaskingStyle] [-s LookupTableSize] [-w MaximalSpan] [-d MinAccessibleLength] Options: (Required) -i STR RNA sequences in FASTA format -o STR The database name (Optional) -r INT Designation of repeat masking style 0:hard-masking, 1:soft-masking, 2:no-masking [default:0] -s INT Lookup table size of short string search [default: 8] -w INT The constraint of maximal distance between the bases that form base pairs. This parameter have to be set to 20 and over. [default: 70] -d INT Minimum accessible length for accessibility approximation [defualt:5] ris: search RNA-RNA interaction between a query and database sequences RIblast ris [-i InputFastaFile] [-o OutputFileName] [-d DatabaseFileName] [-l MaxSeedLength] [-e HybridizationEnergyThreshold] [-f InteractionEnergyThreshold] [-x DropOutLengthInGappedExtension] [-y DropOutLengthInUngappedExtension] [-g OutputEnergyThreshold] [-s OutputStyle] Options: (Required) -i STR RNA sequences in FASTA format -o STR Output file name -d STR The database name (Optional) -l INT Max size of seed length [default:20] -e DBL Hybridization energy threshold for seed search [default: -6.0] -f DBL Interaction energy threshold for removal of the interaction candidate before gapped extension [default: -4.0] -x INT DropOut Length in gapped extension [defualt:16] -y INT DropOut Length in ungapped extension [defualt:5] -g DBL Energy threshold for output [defualt:-8.0] -s INT Designation of output format style 0:simplified output style, 1:detailed output style [defualt:0]
Output file format
RIblast outputs detected interactions as follows. An interaction is expressed in five columns.The first, second, third, fourth and fifth column of an interaction describes intearction id, name of query RNA, name of target RNA, interaction energy of the interaction, and interacted regions ([region in query]:[region in target]), respectively.
RIblast ris result
Id,Query name, Query Length, Target name, Target Length, Accessibility Energy, Hybridization Energy, Interaction Energy, BasePair
Query Length and Target Length means the region of non-repeat region when repeat sequences are masked.
If you need the information of interacted base pair, please designate the output format style as detailed output style.
This software is released under the MIT License, see LICENSE.txt.
2019/11/02 Version 1.2.0 was released. The calculation speed is about twice as fast as before.
2017/11/30 Version 1.1.3 buf fix:calculation of dangling energy.
2017/07/06 Version 1.1.2 I changed output file format.
2016/12/07 Version 1.1.1 I changed output file format.
2016/11/21 Version 1.1.0 was released.
2016/10/10 Version 1.0.2 bug fix: I fixed a bug in accessibility calculation.
2016/09/27 Version 1.0.1 bug fix: I fixed a bug in loading fastafile and calculation of dangling energy. I also changed output file format.
2016/08/31 Version 1.0.0 was released.
Tsukasa Fukunaga and Michiaki Hamada. "RIblast: An ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach." btx287, Bioinformatics (2017)