We use compositional and comparative methods in the analysis of genomic DNA sequence. The comparative methods primarily involve searches for homology within publicly available databases and multiple sequence analyses generated locally. Compositional analysis is concerned with the construction of gene models from computer-predicted exons and exon-splice sites.
Database Searching
Motif searching
Exon prediction and gene modelling programs
tRNA predictions are performed with tRNAScan-SE
Click here for a detailed discussion of our method for identfying putative autonomous and non-autonomous transposons, solo LTRs, and LINEs.
Short tandem repeats or microsatellites are located with RepeatMasker.
Local manipulations of the sequence are performed with the GCG package.
Multiple sequence analysis is also performed with CLUSTALW.
Resources for Arabidopsis phenotypes include Arabidopsis Information Management System (AIMS) and Nottingham Arabidopsis Stock Centre (NASC).
The Kyoto Encyclopedia for Genes and Genomes (KEGG) is a good resource for metabolic pathways.
We also utilize NCBI's Entrez to gather relevant information. Various scripts written in-house are also used.