ASprofile protocols

View ASprofile computational protocol

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chevron_left Alternative splicing events identification Known transcript quantification Differential usage Intron retention detection Exon skipping detection Novel transcript quantification chevron_right
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ASprofile specifications

Information


Unique identifier OMICS_01942
Name ASprofile
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data A set of gene annotations
Input format GTF
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • collect-fpkm
  • extract-as
  • extract-as-fpkm

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Maintainer


  • person_outline Liliana Florea <>

Publication for ASprofile

ASprofile in pipelines

 (8)
2018
PMCID: 5792444
PMID: 29386544
DOI: 10.1038/s41598-018-20373-6

[…] gene structures were refined by comparing known transcripts with the reconstructed transcripts from the six transcriptome sequencing datasets using blast software., as events were detected using asprofile software and were classified into 12 categories: alternative 5′ first exon (transcription start site, tss), alternative 3′ last exon (transcription terminal site, tts), skipped exon (skip), […]

2018
PMCID: 5792444
PMID: 29386544
DOI: 10.1038/s41598-018-20373-6

[…] refined genes is provided in supplementary table ., from the same gene, alternative splicing (as) could generate multiple transcripts, some of which might perform contrasting functions. we used the asprofile software to analyze as events in each library. among all the 12 detected types of as events, alternative first exons (tss) and last exons (tts) were the most common, accounting […]

2018
PMCID: 5915550
PMID: 29720989
DOI: 10.3389/fpls.2018.00500

[…] annotation documents by this software (trapnell et al., ). all transcripts were detected by the method of rabt (reference annotation based transcript) using cufflinks (v2.1.1) (trapnell et al., ). asprofile (v1.0) was applied to classify the alternative splicing (as) events into 12 types, the quantity of which was also calculated (florea et al., ). the analysis of fusion genes and long […]

2017
PMCID: 5506030
PMID: 28698542
DOI: 10.1038/s41598-017-04336-x

[…] could be compared directly., snp and indel analyses were performed by mapping rna-seq reads into the genomic of sus scrofa (sscrofa10.2) using samtools (v1.3.1). the as events for each library using asprofile.b (v1.0.4)., the software deseq (v1.16) was used for differential gene expression analysis between two samples with biological replicates using a model based on the negative binomial […]

2017
PMCID: 5513552
PMID: 28715466
DOI: 10.1371/journal.pone.0181399

[…] novel genes from tophat alignment were constructed using cufflinks v2.1.1 reference annotation based transcript (rabt) assembly method. the alternative splicing events were found by the software of asprofile v1.0. this approach increased 1828 transcripts in antennae (). in total, the sequenced fragments created 21,643 genes, 1,828 of them are novel (). 12,861 of these genes were detected in one […]


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ASprofile in publications

 (22)
PMCID: 5915550
PMID: 29720989
DOI: 10.3389/fpls.2018.00500

[…] annotation documents by this software (trapnell et al., ). all transcripts were detected by the method of rabt (reference annotation based transcript) using cufflinks (v2.1.1) (trapnell et al., ). asprofile (v1.0) was applied to classify the alternative splicing (as) events into 12 types, the quantity of which was also calculated (florea et al., ). the analysis of fusion genes and long […]

PMCID: 5792444
PMID: 29386544
DOI: 10.1038/s41598-018-20373-6

[…] refined genes is provided in supplementary table ., from the same gene, alternative splicing (as) could generate multiple transcripts, some of which might perform contrasting functions. we used the asprofile software to analyze as events in each library. among all the 12 detected types of as events, alternative first exons (tss) and last exons (tts) were the most common, accounting […]

PMCID: 5755334
PMID: 29301488
DOI: 10.1186/s12870-017-1217-x

[…] using cuffcompare. then, we acquired a non-redundant transcript pool []. the isoforms encoded by annotated genes were extracted and used for the next analysis. astalavista, a web server that can extract as events as much as possible, was used to detect as events []. four basic types of as events, including ir, es, ad and aa, were further analysed., to compare the as events among the ten […]

PMCID: 5509646
PMID: 28706200
DOI: 10.1038/s41598-017-05702-5

[…] enriched in were calculated. benjamini-hochberg method was used to correct the obtained p_value. a corrected p_value ≤ 0.05 was considered to represent significant enrichment of genes., asprofile (v1.0) was used to analyze the potential alternative splicing events of each sample, which was classified into 12 categories: alternative 5′ first exon (transcription start site, tss), […]

PMCID: 5467848
PMID: 28604820
DOI: 10.1371/journal.pone.0179491

[…] assembly method was used to construct and identify both known and novel transcripts from tophat alignment results. alternative splicing (as) events were classified to 12 types by the software asprofile (version 1.0) []. the number of as events in each sample was estimated, separately., the reads mapped to each gene were counted by htseq software (version0.5.4, […]


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ASprofile institution(s)
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
ASprofile funding source(s)
Supported in part by the NSF award ABI-1159078 and NIH grants R01-HG006677 and R01-HG006102.

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