Research Projects for Fellows, June 20 - August 6, 2005
P4: Customizing PCAP for Assembly of EST Sequences
| Title: |
Customizing PCAP for Assembly of EST Sequences |
| Mentors: |
Dr. Xiaoqiu Huang |
| Description: |
The PCAP program was developed for assembly of genomic sequences with base quality values and forward-reverse constraints. The default values for the parameters of PCAP were selected for assembly of genomic sequences. PCAP requires that base quality values be part of input. The goal of this project is to customize PCAP for assembly of EST (Expressed Sequence Tag) sequences. The project is suitable for a student with knowledge in Unix systems and Perl. The student will develop a Perl script for generating input files in PCAP format and find proper PCAP parameter values for assembly of EST sequences. |
| Web Resources: |
PCAP |
| References: |
Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003) PCAP: A Whole-Genome Assembly Program, Genome Research, 13: 2164-2170
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