title: Sircah: a tool for the detection and visualization of alternative transcripts.
abstract: 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.
  
  
  BACKGROUND
  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.
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Eoghan D
authors.initials: ED
authors.lastname: Harrington
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003196:Computer Graphics; D008969:Molecular Sequence Data; D022821:RNA Splice Sites / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000235:genetics*; D014584:User-Computer Interface
chemical_list: D022821:RNA Splice Sites; D014157:Transcription Factors