Trimming and clustering sugarcane ESTs
Open Access
- 1 December 2001
- journal article
- Published by FapUNIFESP (SciELO) in Genetics and Molecular Biology
- Vol. 24 (1-4) , 17-23
- https://doi.org/10.1590/s1415-47572001000100004
Abstract
The original clustering procedure adopted in the Sugarcane Expressed Sequence Tag project (SUCEST) had many problems, for instance too many clusters, the presence of ribosomal sequences, etc. We therefore redesigned the clustering procedure entirely, including a much more careful initial trimming of the reads. In this paper the new trimming and clustering strategies are described in detail and we give the new official figures for the project, 237,954 expressed sequence tags and 43,141 clusters.Keywords
This publication has 7 references indexed in Scilit:
- An optimized protocol for analysis of EST sequencesNucleic Acids Research, 2000
- JESAM: CORBA software components to create and publish EST alignments and clustersBioinformatics, 2000
- The TIGR Gene Indices: reconstruction and representation of expressed gene sequencesNucleic Acids Research, 2000
- A Comprehensive Approach to Clustering of Expressed Human Gene Sequence: The Sequence Tag Alignment and Consensus Knowledge BaseGenome Research, 1999
- CAP3: A DNA Sequence Assembly ProgramGenome Research, 1999
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- Complementary DNA Sequencing: Expressed Sequence Tags and Human Genome ProjectScience, 1991