Tutorial Abstract
Tutorial 5: Introduction to PERL Scripting
Title: Using Perl in the Identification of CIS Elements in Promoter Sequences of Rice Genes.
Presenters: Peter Carswell and Yuan Zhang, Ohio Supercomputer Center
Abstract: The Perl programming concepts addressed will be included in a discussion of two problems associated with the genomic sequence analysis of rice. One problem relates to making a master table listing the known and novel cis elements present in all the annotated rice gene promoters. The results of the application PLACE is parsed with Perl scripts to analyze and annotate two hundred seventy known cis Elements in over three thousand different gene promoter sequences of a particular rice genome. Another application, RiCES, is applied to the same set of promoter sequences to look for novel cis Elements. Perl is used for a similar analysis and annotation. The second involves Blast searches of TIGR annotated rice genome against KOME full length cDNAs. Perl and BioPerl are used to prepare the data, as well as, annotate the results of the resulting matches in the BLAST reports. The results are very helpful for researchers doing genomic scale studies of rice genes. Rice is a model monocot plant and share many genes among the other cereal crops like wheat, maize, sorghum. Researchers can do lot of comparative genomic studies using this resource for their genes of interest.