GrailEXP and Genome Analysis Pipeline for Genome Annotation
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Abstract
The Basic Protocol describes the use of GrailEXP, the latest version of the gene finding system from Oak Ridge National Laboratory. GrailEXP provides gene models, by making use of sequence similarity with Expressed Sequence Tags (ESTs) and known genes. GrailEXP also provides alternatively spliced constructs for each gene based on the available EST evidence. The Support Protocol describes the use of the Genome Analysis Pipeline, a web application which allows users to perform comprehensive sequence analysis by offering a selection from a wide choice of supported gene finders, other biological feature finders, and database searches.
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PDF or HTML at Wiley Online LibraryTable of Contents
- Basic Protocol 1: Performing Gene Predictions Using the GrailEXP Web Interface
- Alternate Protocol 1: Using Genome Analysis Pipeline for Comprehensive Analysis of DNA Sequences
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
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PDF or HTML at Wiley Online LibraryMaterials
Basic Protocol 1: Performing Gene Predictions Using the GrailEXP Web Interface
Necessary Resources
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Figure 4.9.1 GrailEXP submission form. View Image -
Figure 4.9.2 Pipeline submission form. View Image -
Figure 4.9.3 Pipeline summary page. View Image -
Figure 4.9.4 GrailEXP genes text table. View Image -
Figure 4.9.5 Java Pipeline Viewer. View Image
Videos
Literature Cited
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