Development of gene-finding algorithms for fungal genomes : dealing with small datasets and leveraging comparative genomics

A computer program called FUNSCAN was developed which identifies protein coding regions in fungal genomes. Gene structural and compositional properties are modeled using a Hidden Markov Model. Separate training and testing sets for FUNSCAN were obtained by aligning cDNAs from an organism to their genomic loci, generating a 'gold standard' set of annotated genes. The performance of FUNSCAN is competitive with other computer programs design to identify protein coding regions in fungal genomes. A technique called 'Training Set Augmentation' is described which can be used to train FUNSCAN when only a small training set of genes is available. Techniques that combine alignment algorithms with FUNSCAN to identify novel genes are also discussed and explored.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2003

Author dc:creator

• Lazarovici, Allan, 1979-

Advisor dc:contributor.advisor

• Christopher Burge.

• Electrical Engineering and Computer Science.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/29681

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/29681