Literature DB >> 18635569

Sircah: a tool for the detection and visualization of alternative transcripts.

Eoghan D Harrington1, Peer Bork.   

Abstract

UNLABELLED: Sircah is a flexible tool for the detection, analysis and visualization of alternative transcripts. It takes as input gene models or spliced alignments and creates a database of alternative transcription events: alternative transcription initiation and polyadenylation, alternative 3' and 5' splice-site usage, skipped exons and retained introns. The results can be visualized in a variety of ways, allowing the creation of publication quality images. AVAILABILITY: The Sircah is available for download under a creative commons license along with additional documentation and a tutorial from http://www.bork.embl.de/Sircah.

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Year:  2008        PMID： 18635569     DOI： 10.1093/bioinformatics/btn361

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  7 in total

1.  Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii.

Authors:  Adam Labadorf; Alicia Link; Mark F Rogers; Julie Thomas; Anireddy Sn Reddy; Asa Ben-Hur
Journal:  BMC Genomics       Date:  2010-02-17       Impact factor: 3.969

2.  Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements.

Authors:  Anireddy S N Reddy; Mark F Rogers; Dale N Richardson; Michael Hamilton; Asa Ben-Hur
Journal:  Front Plant Sci       Date:  2012-02-07       Impact factor: 5.753

3.  Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing.

Authors:  Dale N Richardson; Mark F Rogers; Adam Labadorf; Asa Ben-Hur; Hui Guo; Andrew H Paterson; Anireddy S N Reddy
Journal:  PLoS One       Date:  2011-09-14       Impact factor: 3.240

4.  SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.

Authors:  Mark F Rogers; Julie Thomas; Anireddy Sn Reddy; Asa Ben-Hur
Journal:  Genome Biol       Date:  2012-01-31       Impact factor: 13.583

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

Authors:  Mandana Baharlou Houreh; Payam Ghorbani Kalkhajeh; Ali Niazi; Faezeh Ebrahimi; Esmaeil Ebrahimie
Journal:  Sci Rep       Date:  2018-03-22       Impact factor: 4.379

6.  Vials: Visualizing Alternative Splicing of Genes.

Authors:  Hendrik Strobelt; Bilal Alsallakh; Joseph Botros; Brant Peterson; Mark Borowsky; Hanspeter Pfister; Alexander Lex
Journal:  IEEE Trans Vis Comput Graph       Date:  2016-01       Impact factor: 4.579

7.  Comparative evaluation of intron prediction methods and detection of plant genome annotation using intron length distributions.

Authors:  Long Yang; Hwan-Gue Cho
Journal:  Genomics Inform       Date:  2012-03-31
  7 in total

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