Seminars & Events

Mathematics and Computer Science Division
"Computational tools for annotating metagenomic sequences: FragGeneScan and SWIFT"

DATE: February 22, 2010
TIME: 10:30 AM - 11:30 AM
SPEAKER: Yuzhen Ye, Assistant Professor at the School of Informatics and Computing, Indiana University, Bloomington
LOCATION: Bldg: 240, Conference Room 4301, Argonne National Laboratory
HOST: Folker Meyer

Description:
We have developed several computational tools for metagenomic sequence annotation. I will mainly talk about FragGeneScan and SWIFT. FragGeneScan is a tool for (fragmental) gene prediction from short reads. It is based on a Hidden Markov Model (HMM) that incorporates the frame-shift-causing sequencing errors. We have tested FragGeneScan on simulated short reads as well as reads from metagenomic projects, and the results show that FragGeneScan outperforms other gene predictors on very short reads, and reads with sequencing errors. SWIFT is a tool for fast protein similarity search, which achieves speedup by utilizing reduced amino acid alphabet and flexible seeds. SWIFT achieves up to ~40 times speedup as compared to BLAST at the cost of a small loss of similarity detection sensitivity for short reads.

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