BPG is committed to discovery and dissemination of knowledge
Home / Archive / Volume 13, Issue 10
  • This Article
Peer-Review Report of This Article
Academic Rules and Norms of This Article
Citation of this article
Corresponding Author of This Article
Research Domain of This Article
Article-Type of This Article
Open-Access Policy of This Article
Times Cited Counts in Google of This Article
Journal Information of This Article
Publication Name
World Journal of Stem Cells
ISSN
1948-0210
Publisher of This Article
Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

Review
©The Author(s) 2021.
World J Stem Cells. Oct 26, 2021; 13(10): 1394-1416
Published online Oct 26, 2021. doi: 10.4252/wjsc.v13.i10.1394
Table 2 Alternative splicing analysis tools based on isoform-based method and count-based method (including the exon- and event-based approaches)
Tools
Human/ plants/ animals
Types of detecting splices
Type of tool
Year of publish
Ref.    
Citation
Isoform-based method
Cuffdiff2All-Linux2012[109]9550
HMMSplicerAll-Linux2010[110]79
PennDiffAll-Linux2018[111]9
rSeqDiffAll-R2013[112]29
DiffSpliceAll-Windows/Linux2013[113]141
NSMAPAll-MatLab package2011[114]46
MISOAllSE / A3SS / A5SS / MXE / TandemUTR / RI / AF / ALLinux2010[115]1166
Exon-based method
TopHaTAll-Linux2009[116]11026
DEXSeqAll-R2012[117]1091
edgeRAll-R2010[118]19012
JunctionSeqAll-R2016[119]81
limmaAll-R2015[120]11033
rSeqNPAll-R2015[121]10
Event-based method
MAJIQAllSE / A5SS / A3SSLinux2016[122]171
rMATSAllSE / A5SS / A3SS / RI / MXELinux2014[123]746
SUPPAAllSE / A5SS / A3SS / RI / MXE / AF / ALLinux2015[124]134
SUPPA2AllSE / A5SS / A3SS / RI / MXE / AF / ALLinux2018[125]-
ASGALAllSE / A5SS / A3SS / RILinux2018[126]12
Astalavista version 3.0AllSE / A5SS / A3SS / RILinux2012[127]62
LeafCutterAllSE / A5SS / A3SSLinux2018[128]200
SpliceGrapherAllSE / A5SS / A3SS / RILinux2012[129]132
KisSpliceAllSNPs, indels and AS events (SE / A5SS / A3SS / RI )Linux2012[130]-
Alt Event FinderAllSELinux2012[131]24
MattAllSE / A5SS / A3SS / RILinux2018[132]14
ALEXA-seqAllSE / A5SS / A3SS / RILinux2010[133]340
OutriggerAllSE / A5SS / A3SS / RILinux2016[134]86
ASDTAllSE / A5SS / A3SS / RIPerl2018[135]5
SplicePieAllSE / RIR2015[136]17
VAST-TOOLSAllSE / A5SS / A3SS / RIR2017[137]118
spliceRAllSE / A5SS / A3SS / RI / AF/ALR2014[138]80
Pro-SplicerHumanSE / A5SS / A3SSWebsite (http://prosplicer.mbc.nctu.edu.tw/)2003[139]50
ASPicDBHumanSE / A5SS / A3SS / RI / AF/ALWebsite (http://srv00.recas.ba.infn.it/ASPicDB/)2006[140]33
H-DBASHumanSE / A5SS / A3SS / RI / AF/ALWebsite (http://www.h-invitational.jp/h-dbas/)2007[141]56
ASIPPlantSE / A5SS / A3SS / RIWebsite (http://www.plantgdb.org/ASIP/)2006[142]535
ASGHumanSE / A5SS / A3SS / RIWebsite (https://brcwebportal.cos.ncsu.edu/asg/)2004[143]116
VastDBvertebrateSE / A5SS / A3SS / RIWebsite (https://vastdb.crg.eu/wiki/Main_Page)2017[137]118
AstalavistaHuman/ AnimalsSE / A5SS / A3SS / RIWebsite (http://astalavista.sammeth.net/)2007[144]205
SpliceDitectorPlant/ HumanSE / A5SS / A3SS / RIWindows2018[11]1
dSpliceTypeAllSE / A5SS / A3SS / RI / MXEWindows/ Linux2015[145]4
AltAnalyzeAllSE / A5SS / A3SS / RI / MXEWindows/ Linux2010[146]253
SE: Skipped exon; A3SS: Alternative acceptor site; A5SS: Alternative donor site; RI: Retained intron; MXE: Mutually exclusive exons; AF/AL: Alternative first/last exons.
Full Size Table
Write to the Help Desk
Copyright © 1993-2026 Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA. All rights reserved, including rights relating to text and data mining, AI training, and similar technologies. For open-access content, the applicable copyright and licensing terms govern.