ASPic-GeneID: A Lightweight Pipeline for Gene Prediction and Alternative Isoforms Detection
Joint Authors
Picardi, Ernesto
Alioto, Tyler
Guigó, Roderic
Pesole, Graziano
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-11-07
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
New genomes are being sequenced at an increasingly rapid rate, far outpacing the rate at which manual gene annotation can be performed.
Automated genome annotation is thus necessitated by this growth in genome projects; however, full-fledged annotation systems are usually home-grown and customized to a particular genome.
There is thus a renewed need for accurate ab initio gene prediction methods.
However, it is apparent that fully ab initio methods fall short of the required level of sensitivity and specificity for a quality annotation.
Evidence in the form of expressed sequences gives the single biggest improvement in accuracy when used to inform gene predictions.
Here, we present a lightweight pipeline for first-pass gene prediction on newly sequenced genomes.
The two main components are ASPic, a program that derives highly accurate, albeit not necessarily complete, EST-based transcript annotations from EST alignments, and GeneID, a standard gene prediction program, which we have modified to take as evidence intron annotations.
The introns output by ASPic CDS predictions is given to GeneID to constrain the exon-chaining process and produce predictions consistent with the underlying EST alignments.
The pipeline was successfully tested on the entire C.
elegans genome and the 44 ENCODE human pilot regions.
American Psychological Association (APA)
Alioto, Tyler& Picardi, Ernesto& Guigó, Roderic& Pesole, Graziano. 2013. ASPic-GeneID: A Lightweight Pipeline for Gene Prediction and Alternative Isoforms Detection. BioMed Research International،Vol. 2013, no. 2013, pp.1-11.
https://search.emarefa.net/detail/BIM-1030604
Modern Language Association (MLA)
Alioto, Tyler…[et al.]. ASPic-GeneID: A Lightweight Pipeline for Gene Prediction and Alternative Isoforms Detection. BioMed Research International No. 2013 (2013), pp.1-11.
https://search.emarefa.net/detail/BIM-1030604
American Medical Association (AMA)
Alioto, Tyler& Picardi, Ernesto& Guigó, Roderic& Pesole, Graziano. ASPic-GeneID: A Lightweight Pipeline for Gene Prediction and Alternative Isoforms Detection. BioMed Research International. 2013. Vol. 2013, no. 2013, pp.1-11.
https://search.emarefa.net/detail/BIM-1030604
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1030604