A Hybrid, Recursive Algorithm for Clustering Expressed Sequence Tags in Chlamydomonas reinhardtii

Author

Jain, Monica ; Holz, Hilary ; Shrager, Jeff ; Vallon, Olivier ; Hauser, Charles ; Grossman, Arthur

Author_Institution

Dept. of Plant Biol., Carnegie Inst. of Washington, Stanford, CA

Volume

3

fYear

0

fDate

0-0 0

Firstpage

404

Lastpage

407

Abstract

We present an efficient, fully automated algorithm to assemble ESTs into full-length cDNA sequences that represent the complete coding regions of a gene. Our EST clustering algorithm is neither hierarchical nor incremental, but recursive, processing each EST once. The algorithm exploits a variety of syntactic and statistical features of the ESTs. The resulting assembly shows significant improvement in computational efficiency and information extraction over a previous assembly of C. reinhardtii ESTs. The algorithm was developed using iterative and participatory design on C. reinhardtii; however, it can be used for any organism with a draft genomic sequence

Keywords

DNA; botany; genetics; pattern clustering; Chlamydomonas reinhardtii; cDNA sequences; expressed sequence tag clustering; recursive algorithm; Algorithm design and analysis; Assembly; Bioinformatics; Cloning; Clustering algorithms; DNA; Genomics; Iterative algorithms; Sequences; Technical Activities Guide -TAG;

fLanguage

English

Publisher

ieee

Conference_Titel

Pattern Recognition, 2006. ICPR 2006. 18th International Conference on

Conference_Location

Hong Kong

ISSN

1051-4651

Print_ISBN

0-7695-2521-0

Type

conf

DOI

10.1109/ICPR.2006.87

Filename

1699550