Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic features.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Standard gene-finding methods struggle with small proteins, regulatory elements, and functional RNAs due to size limitations, sequence variation, and lack of complete gene catalogs.
• Conserved sequences across related organisms offer valuable information for identifying missed functional elements.
• Existing tools like ORF-finders and pattern matchers have limitations in detecting all functional genomic sequences.

Purpose of the Study:

• To develop and present a novel computational method, tricross, for detecting conserved functional sequences across multiple genomes.
• To identify genes and other potentially functional sequences that may be missed by standard bioinformatics software.
• To utilize conserved sequence information for enhanced genomic analysis.

Main Methods:

• The tricross software performs multi-way cross-comparisons of sequence sets to identify conserved regions.
• It generates graphical representations (VRML) and alignments of conserved sequence triples.
• The method can be applied to both intergenic and gene sequences, and to pairs or triplets of genomes.

Main Results:

• Tricross identified 101 intergenic sequences conserved among three Pyrococcus archaeal genomes.
• Of these, 29 contained small RNA molecules, a recently discovered class in Archaea.
• The remaining 72 sequences included conserved promoter elements and others of unknown significance.
• The software also generated inter-genomic gene order dot-plots for various bacterial species.

Conclusions:

• The tricross method effectively identifies conserved functional sequences, including small RNAs and promoters, that are often missed by conventional approaches.
• This cross-genomic comparison strategy enhances the discovery of novel genomic elements.
• Tricross is a versatile tool applicable to diverse genomic comparison tasks.