SpringerProtocols: Abstract: 5. Expressed Sequence Tags: Analysis and Annotation

5. Expressed Sequence Tags: Analysis and Annotation

By: John Parkinson², Mark Blaxter²

Abstract

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Expressed sequence tags (ESTs) present a special set of problems for bioinformatic analysis. They are partial and error-prone, and large datasets can have significant internal redundancy. To facilitate analysis of small EST datasets from in-house projects, we present an integrated “pipeline” of tools that take EST data from sequence trace to database submission. These tools also can be used to provide clustering of ESTs into putative genes and to annotate these genes with preliminary sequence similarity searches. The systems are written to use the public-domain LINUX environment and other openly available analytical tools.

Affiliation(s): (2) Institute of Cell, Animal, and Population Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK

Book Title: Parasite Genomics Protocols

Series: Methods in Molecular Biology | Volume: 270 | Pub. Date: May-17-2004 | Page Range: 93-126 | DOI: 10.1385/1-59259-793-9:093

Subject: Genetics/Genomics

Key Words: BLAST - expressed sequence tags - LINUX annotation - sequence analysis

References

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