Visualization of aligned genomic open reading frame data*

Abstract

Students can better appreciate the value of genomic data if they are asked to use the data themselves. However, in general the enormous volume of data involved makes detailed examination difficult. Here we present a web site that allows students to study one particular aspect of sequenced genomes. They are able to align the open reading frames (ORFs) of any available genome that is of reasonable size. The ORFs may be aligned using either the start codon or the stop codon as the starting points. Results will readily show the presence of common ribosome binding sites as well as reveal interesting order within the ORFs that is nonexistent outside of them. Students will be able to ask various questions involving comparisons of genomes and see the results presented in both a tabular and graphic format. An example problem is presented under "Results."Keywords: Alignment, visualization, genomes, ORF.The past few years have seen an explosion of DNA sequencing results. In particular, entire genomes, both prokaryotic and eukaryotic, are now available for study due to rapid advances in sequencing methodologies. The first viral sequence, phi-X174, was published in 1977 and consisted of 5386 bases in a single-stranded genome [1]. The first eubacterial sequence, Haemophilus influenzae, was completed in 1995 and was 1,830,137 base pairs long [2]. Yeast and human draft sequence lengths testify to the power of the available methods and the quantity of information produced. However, the enormous size of even the simplest genomes sometimes hinders easy use of the available data.Students are presented with information relating to cis elements affecting transcription and translation by several different methods. The most common is a simple presentation of "consensus" data. For a more detailed appreciation, they are given tables of aligned sequences of these elements. Recent statistical approaches have provided a more accurate way to present summaries of the data. Two related methods are based on a maximum likelihood statistic. One involves a weight matrix [3], and the other involves an information theory approach [4]. Both methods have their proponents and virtues [5,6]. A typical output shows cis sites in terms of varying sizes of base logos (see Ref. 7 for example).Here we present an alternate way to display and examine alignable sequence data. We take advantage of the availability of genomic data to show that open reading frames (ORFs) 1 from entire genomes can be aligned to reveal global patterns in DNA data. We present a web site where students can ask their own questions about sequences and produce the results quickly.