Creating a Workflow For Expressed Sequence Tags Analysis
Document Type
Conference Proceeding
Publication Date
12-1-2008
School
Computing Sciences and Computer Engineering
Abstract
Expressed sequence tags (ESTs) are short sequence fragments of genes and may be used in genomic and genetic investigations. Despite rapid expansion of EST generation process, the resulting sequences are relatively low quality fragments and need to be cleaned before assembling into a larger sequence by identifying overlaps between sample sequences. EST comparative analysis and functional assignment then should be performed to characterize gene annotation and classification, and describe gene functions. In this study we reported the establishment of a workflow for analysis and assembly of ESTs sequences into contigs and singlets and implementation of an EST database. High quality assembled ESTs were annotated using BLASTX through our local BLAST server. We searched several databases including the NCBI non-redundant protein databases. The BLAST results were automatically extracted and transferred into a relational database. We used well annotated Gene Ontology (GO) information to characterize gene function annotation and to classify molecular function, biological processes, and cellular communication. Pathway analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) classification has been used for pathway mapping. Enzyme commission (EC) numbers were used to determine which sequences pertained to a specific pathway.
Publication Title
Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
First Page
806
Last Page
808
Recommended Citation
Pirooznia, M.,
Gong, P.,
Zhang, C.,
Perkins, E.,
Deng, Y.
(2008). Creating a Workflow For Expressed Sequence Tags Analysis. Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008, 806-808.
Available at: https://aquila.usm.edu/fac_pubs/17944