AStalavista protocols

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AStalavista specifications

Information


Unique identifier OMICS_01943
Name AStalavista
Alternative name Alternative Splicing TrAscriptional LAndscape VISualization Tool And more
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 4.0
Stability Stable
Maintained Yes

Subtools


  • ASTA
  • ASTAFUNK
  • SCORER
  • VISTA

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Documentation


Maintainers


  • person_outline Sylvain Foissac <>
  • person_outline Michael Sammeth <>

Additional information


http://sammeth.net/confluence/display/ASTA/1+-+Introduction

Information


Unique identifier OMICS_01943
Name AStalavista
Alternative name Alternative Splicing TrAscriptional LAndscape VISualization Tool And more
Interface Web user interface
Restrictions to use None
Input data A set of transcripts with known exon–intron structure (e.g. from mRNAs or ESTs) or a list of genes/transcripts/proteins IDs.
Input format GTF, TXT
Output data A result page showing a list where each event type is depicted and its unique code in the relative-position notation is given and a graphical overview in form of a pie diagram that displays the distribution of events across the groups, considering differentially each type of simple event and pooling the others in one group.
Output format GTF, ASTA
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • ASTA
  • ASTAFUNK
  • SCORER
  • VISTA

Documentation


Maintainers


  • person_outline Sylvain Foissac <>
  • person_outline Michael Sammeth <>

Additional information


http://sammeth.net/confluence/display/ASTA/1+-+Introduction

Publications for Alternative Splicing TrAscriptional LAndscape VISualization Tool And more

AStalavista in pipelines

 (5)
2018
PMCID: 5755334
PMID: 29301488
DOI: 10.1186/s12870-017-1217-x

[…] of expressed genes in the ten tissues ranged from 17,859 (tendril) to 18,572 (root) (table ). moreover, 3344 new genes were detected, which produced 5173 transcripts.table 2, we applied the program astalavista [] to identify the as events in cucumber. according to the current annotation, we analysed only the as events occurring on the transcripts encoded by the annotated genes. a total […]

2017
PMCID: 5575331
PMID: 28852064
DOI: 10.1038/s41598-017-10143-1

[…] we required lncrnas to be induced or repressed in all three replicated samples due to their stochastic expression., alternative splicing (as) events were identified from the expressed isoforms using astalavista. different types of as events were extracted and counted as previously described. briefly, we searched for four categories of as events, included exon skipping, alternative 5′ donor […]

2016
PMCID: 5001199
PMID: 27557137
DOI: 10.1186/s12864-016-2901-1

[…] and fdr<0.05 were as the threshold in this study to select differentially expressed genes between high and low yielders., the alternative splicing transcriptional landscape visualization tool (astalavista) web server (http://genome.crg.es/astalavista/) extracts and displays splice events from genomic annotation of exon-intron gene coordinates. astalavista v3.0 [] was employed to identify […]

2014
PMCID: 4287496
PMID: 25209012
DOI: 10.1186/1471-2164-15-780

[…] with expression levels less than 5% of the most abundant transcript format from a gene, were filtered out before as detection. transcripts that remained in both replicates were subjected to astalavista web server to discover as events []. as transcripts were extracted from each as event and the percentage of as transcripts was calculated through dividing the number of as transcripts […]

2013
PMCID: 3753335
PMID: 23990983
DOI: 10.1371/journal.pone.0071763

[…] v1.3.0 – reference annotation based transcript (rabt) assembly method was used to construct and identify both known and novel transcript fragments (transfrags) from tophat alignment results. astalavista v2.2 was used to estimate the five basic alternative splices (ass) events both in and among the groups based on the results of cuffmerge and cuffcompare modules in cufflinks package . […]


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AStalavista in publications

 (48)
PMCID: 5915550
PMID: 29720989
DOI: 10.3389/fpls.2018.00500

[…] and sixth chromosomes (supplemental figure ). a total of 87 lncrnas were found by both cpc and pfam analysis (figure )., five kinds of alternative splicing (as) events were identified by using astalavista analysis (http://genome.crg.es/astalavista/faq.html). a total of 137,831 as events were found in barley based on pacbio reads and corresponding annotated gene models, which occurred […]

PMCID: 5836289
PMID: 29541089
DOI: 10.3389/fpls.2018.00277

[…] genes among different studies were identified. a custom made in-house perl script was employed for gene selection and mapping., the alternative splicing events of each samples were predicted by the astalavista program () on the web server using the gtf files generated by cufflinks. differential splicing analysis was done using miso version 0.5.3 () and rmats version 4.0.1 () using the default […]

PMCID: 5782385
PMID: 29361913
DOI: 10.1186/s12864-018-4449-8

[…] lc leaf well-watered control, ls leaf salt-stressed treatment, rc root well-watered control, rs root salt-stressed treatment, lc leaf well-watered control, ls leaf salt-stressed treatment, we used astalavista to identify and classify the different types of alternative splicing. a total of 14,172 as events were identified from 6798 genes in all 40 libraries, implying that nearly 31.58% […]

PMCID: 5793194
PMID: 29346292
DOI: 10.3390/genes9010043

[…] exon (mee), and intron retention (ir) (a). several as identifiers have been developed, such as a program to assemble spliced alignments (pasa) [], splicegrapher [], cash [], and the method of astalavista et al. [] to delimitate gene structure (). the as event is surprisingly common in sorghum (10,053) [], amborella (4879) [], and bamboo (21,154) [] ()., single-molecule long read […]

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

[…] reference genome structure annotation 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., […]


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AStalavista institution(s)
Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Laboratory for Scientific Computing, Petrópolis, Rio de Janeiro, Brazil
AStalavista funding source(s)
Supported by the National Counsel of Technological and Scientific Development (CNPq) by grant 132455/2013-7 and 140941/2015-0 as well as grant 310132/2015-0, and from the Research Support Foundation of the State of Rio de Janeiro (FAPERJ) by grant E_06/2015.

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