SpliceSeq statistics

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SpliceSeq specifications

Information


Unique identifier OMICS_01267
Name SpliceSeq
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input format FASTA, FASTQ
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.1
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Michael C. Ryan

Publication for SpliceSeq

SpliceSeq citations

 (8)
call_split

SpliceDetector: a software for detection of alternative splicing events in human and model organisms directly from transcript IDs

2018
Sci Rep
PMCID: 5864913
PMID: 29567976
DOI: 10.1038/s41598-018-23245-1
call_split See protocol

[…] ting tool constructs the SpliceGraph by summarizing short reads aligned to a reference genome. SplAdder integrates annotation information and RNA-Seq data to generate an augmented splicing graph, and SpliceSeq summarizes known transcript variations and knowledge about gene structure into a directed acyclic graph. Requiring a prerequisite data as a reference data is a noticeable clue in all of thes […]

library_books

Radiation induced alternative transcripts as detected in total and polysome bound mRNA

2017
Oncotarget
PMCID: 5787501
PMID: 29416646
DOI: 10.18632/oncotarget.21672

[…] The bioinformatics program SpliceSeq, which was developed for alternative splicing analysis of RNA-Seq data [], was used to identify differential splicing events in polysome-bound RNA and total RNA. SpliceSeq returns gene reads […]

library_books

DART: a fast and accurate RNA seq mapper with a partitioning strategy

2017
Bioinformatics
PMCID: 5860201
PMID: 28968831
DOI: 10.1093/bioinformatics/btx558

[…] ns one or more introns and concatenate adjacent or distant exons, which may result in the alignment not contiguous and separated by large gaps. Though some RNA-Seq mappers, such as Erange (), OSA (), SpliceSeq (), etc.) align reads against a transcriptome to avoid introns in the reference, the gene annotation is incomplete for most of the studied organisms. Alignments based on the transcriptome wo […]

library_books

Next generation profiling to identify the molecular etiology of Parkinson dementia

2016
PMCID: 4881621
PMID: 27275011
DOI: 10.1212/NXG.0000000000000075

[…] SpliceSeq identified significant disease-associated differences in transcript variants. SpliceSeq-predicted events were initially filtered for significance (p < 0.01) and dPSI > |0.2|, where dPSI is t […]

library_books

A survey of best practices for RNA seq data analysis

2016
Genome Biol
PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] ples is small (Figure S1d in Additional file ). Sashimi, structure, and hive plots for splicing quantitative trait loci (sQTL) can be obtained using SplicePlot []. Splice graphs can be produced using SpliceSeq [], and SplicingViewer [] plots splice junctions and alternative splicing events. TraV [] is a visualization tool that integrates data analysis, but its analytical methods are not applicable […]

library_books

A serine–arginine rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii

2015
Nucleic Acids Res
PMCID: 4482073
PMID: 25870410
DOI: 10.1093/nar/gkv311

[…] lly, we attempted to determine the extent of alternative splicing in individual samples. Again, there were no existing programs that suited our needs. Some programs, such as ALEXA-Seq, SpliceTrap and SpliceSeq, are dependent on curated datasets specific to the human genome (–), while others, such as SOLAS and MISO, require transcript models to function (,). By creating a program that focused purel […]

Citations

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SpliceSeq institution(s)
In Silico Solutions, Fairfax, VA; Department of Bioinformatics and Computational Biology and Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

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