A new way of seeing genomesCombining sequence- and signal-based genome analysesCombining sequence- and signal-based genome analyses

Maik Friedel, Thomas Wilhelm, Jürgen SühnelFLI

Introduction: So far, genome analysis is almost exclusively done by treating the sequence as a character string. We developed a new approach that may lead to an improved understanding of nucleotide sequences. Our genome browser encodes the sequence by geometrical or physicochemical dinucleotide properties. The values of these properties are plotted as a dinucleotide-based sequence graph. This type of visualization allows to recognize sequence patterns that are hidden in the usual character string representation. The graph can be manipulated in real time by zooming in and out, changing the amplitude, and by smoothing the graph adopting a shifting window technique. GenBank annotations such as exons, introns etc. can be visualized by different colors. The browser also allows to search for motifs in general and for repeats in particular, both at the character-based sequence and the signal levels. Finally, it offers a number of options for statistical analysis. In summary, the new genome browser is a powerful new tool for enhanced genome analysis. This leads to deeper insights into organization and function of the genome. For providing a reliable basis of dinucleotide property sets we have collected more than 100 in the dinucleotide property database DiProDB (diprodb.fli-leibniz.de).

Conclusion:

The genome browser DiProGB is a powerful new tool for motif discovery in genomes. In addition to the standard sequence representation the DNA is also analyzed considering thermodynamical and geometrical dinucleotide properties which we have collected in the new database DiProDB. This allows to identify and visualize a broad range of both known and unknown genome patterns. The new way of seeing the genome can lead to a better understanding of its organization and function.

1. Visualization of evolutionary events

The DiPro- genome browser can be used to distinguish between 3 types of rRNA gene clusters in chloroplast genomes. The patterns can be best seen applying the free energy change dataset set for the DNA double strand.

2. Visualization of gene and exon/intron organization

With help of the DiPro- genome browser it can be shown that genes tend to be purine-rich. In the Figures shown below the sequence (positive strand) is encoded by the purine content. On the left side all genes of the + strand and on the right side all genes of the – strand are shown in red.

3. Repeats which cannot be found by standard repeat search methods

We have shown this by hiding DNA sequence repeats in an artificial sequence with only 50% alignment identity. The new sequence contains the same repeats that are only visible in the signal representation.

Applications

The exon (red) and intron (green) structure of a given gene can be seen adopting a GC content representation. Exons tend to have a higher GC content than introns.

1.)

Inverted Repeats (25kB)

79 of 88 genomes

2.)

Inverted Repeat Lacking Clade

7 of 88 genomes

3.)

3 Directed Repeats

2 of 88 genomes(subclass: Euglenozoa)

1.) original sequence repeats

2.) the same repeats hidden in an artificial sequence with only 50% sequence identity

The genome browser is a computer program that converts DNA sequences into a signal representation by applying dinucleotide parameters and smoothing the signal using a shifting window technique.

Basic features:• standalone computer program written in C++ • uploads nucleotide sequences of any size and type as

GenBank, (multiple) FASTA or text files• coloring of annotated features of a GenBank file• manipulating the signal in real time

(smoothing, changing amplitude, zooming)

Implemented tools:• motif and repeat search at the signal and

sequence levels• statistical tools for average statistics• random sequence generator• dinucleotide properties editor• editor for searching and sorting the

list of annotated features• editor for adding features and

qualifiers to an existing GenBank file

• export functions for signal information and for the

character-based sequence

DiProGBDiProGB

Basic features: includes more than 100 dinucleotide property sets full references for all sets all sets are classified according to:

- nucleic acid type (DNA, RNA, ...)- strand (double, single)- mode of property determination (experimental, calculated)- property type (thermo dynamical, conformational, letter based)

all information is shown in one table which can be customized users can submit own datasets

Implemented tools: search and sorting functions data export as text file or input file for the Genome Browser Pearson’s correlation and Spearman’s rank

correlation

31.1CG

35.8AC

33.4AT

33.4CC

39.3GA

40TA

36.9TG35.8TT

35.8GT

38.3GC

36.9CA

30.5AG

39.3TC

33.4GG

30.5CT

35.8AA

Example:twist (B-DNA) [degree] (Gorin et al. J. Mol. Biol. 247, 34-48 (1995)).

DiProDBDiProDB

Motif finder Repeat finder

The main window of the genome browser consists of three panel:

(1) Control Panel: uploading and manipulating of sequence information and coding parameter

(2) Main Window: signal curve display(3) Position Panel: position information of the actually depicted sequence range

(part of E. coli K12 genome; applied dinucleotide property: stacking energy)

(main table showing a list of twist parameter sets)

Genome Browser

Database

Ureaplasma parvum serovar 3 str.

Euglena gracilis chloroplast (76235-81341)

Euglena gracilis chloroplast

Pinus thunbergii chloroplast

Saccharum officinarum chloroplast