GrailEXP and Genome Analysis Pipeline for genome annotation
Edward C Uberbacher1, Doug Hyatt, Manesh Shah
1Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Current Protocols in Bioinformatics
|April 23, 2008
Summary
GrailEXP, a gene finding system, identifies gene models using sequence similarity with expressed sequence tags (ESTs) and known genes. A genome analysis pipeline offers comprehensive sequence analysis with various gene finders and database searches.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Gene finding is crucial for understanding genome function.
- Accurate gene models are essential for biological research.
- Existing gene finding tools have limitations in identifying alternative splicing.
Purpose of the Study:
- To introduce GrailEXP, an advanced gene finding system.
- To describe a web-based Genome Analysis Pipeline for comprehensive sequence analysis.
- To leverage expressed sequence tags (ESTs) and known genes for improved gene model prediction.
Main Methods:
- Utilizing sequence similarity with ESTs and known genes for gene model prediction.
- Employing GrailEXP for identifying gene structures and alternative splicing.
- Implementing a Genome Analysis Pipeline with multiple gene finders and database search options.
Main Results:
- GrailEXP successfully generates gene models based on sequence homology.
- Alternative spliced constructs are identified using available EST evidence.
- The Genome Analysis Pipeline facilitates integrated sequence analysis.
Conclusions:
- GrailEXP enhances gene finding accuracy and alternative splicing identification.
- The Genome Analysis Pipeline provides a versatile platform for genomic research.
- These tools advance the field of computational genomics and gene discovery.
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