BACKGROUND
with the rapid growth in the number of sequenced genomes has come a corresponding proliferation of computational tools for viewing, comparing and searching genome sequences and annotations.
tools can be divided into two broad categories  <cit> , database-client and stand-alone.
in general, database-client tools offer static  visualizations of small sets of predefined genomes, while stand-alone tools allow interactive visualizations of locally stored genomes.
stand-alone tools can serve as graphical front ends for displaying the output of locally run calculations.
a high level comparison of common features for these stand-alone tools  <cit>  is shown in table  <dig> and reveals several trends and patterns.
almost all of the tools are implemented in an interpreted language .
while this provides for cross platform portability, the responsiveness  of these applications is poor.
while all of the tools can display genome annotations, additional functionalities  vary widely between programs.
aprograms that use java, tcl/tk and perl are expected to run on any operating system.
bcommon file formats include the genbank flat file , embl flat file , nucleic acid sequence file , general feature format  and protein table file .
a complete list of genome annotation file formats can be found on the genomorama project webpage.
cthe graphic output format labeled "printer" indicates direct output to an attached printer.
not content with the performance or feature set of existing programs, we wrote genomorama, a stand-alone tool originally developed to assist in computational signature design for bacterial and viral pathogen detection.
genomorama allows users designing dna-based hybridization assays, such as pcr or dna probes, to easily identify the regions of a genome targeted by a given assay.
it is distinguished from existing tools by dna hybridization-based sequence searching, its rapid execution speed, and ability to read and export a diverse set of common file formats.
despite its origins as a viewer for viral and bacterial genomes, genomorama can also visualize large eukaryotic genomes .
implementation
genomorama is a software program for interactively displaying and analyzing multiple genomes.
it provides a powerful yet easy to use interface that leverages the visualization power of modern computers  and the substantial bioinformatic infrastructure provided by the ncbi .
genomorama is written in portable, highly optimized c++ and comes in three "flavors" that allow it to run natively on  modern operating systems: os x , microsoft windows  and linux .
the motif version allows any x-windows client that supports opengl to remotely run genomorama.
executables and source code are freely provided for all flavors.
RESULTS
to visualize and compare annotated genome features at all relevant size scales, genomes are displayed on the computer screen as linear, scale-dependent maps.
the user interacts with a map using the mouse, keyboard and scroll bars.
semantic zooming  <cit>  is used to display genomic features which occur at a wide range of scales, i.e.
~ <dig> bases for a mammalian gene, ~ <dig> bases for a pathogenicity island, ~ <dig> bases for a bacterial gene, ~ <dig> bases for a trna, ~ <dig> bases for a transcription factor binding site and  <dig> for a single nucleotide polymorphism.
optional 2d graphs, including %g+c, gc skew  and external data sets , can be superimposed on genome maps.
publication quality, wysiwyg  images can be saved in either gif or postscript formats.
genome annotations and sequences are available in a large number of file formats and genomorama can read a substantial subset of these formats, including genbank , european molecular biology laboratory , abstract syntax notation one , protein table  and fasta.
unlike existing programs, genomorama can read the multi-part gbk, embl and asn.
<dig> files used to store annotations and sequence for partially assembled sequences for both prokaryotic and eukaryotic organisms.
the ability to load multipart annotation files allows access to preliminary annotation information provided by sequencing centers during the whole genome shotgun sequencing of an organism .
a screen shot of five contigs and associated sequencing quality scores from the genome sphingopyxis alaskensis rb <dig> is shown in figure  <dig>
genomorama can load large  genomes.
support for large genomes is crucial for visualizing entire eukaryotic chromosomes.
a comparison between loading times for genomorama and two java-based visualization tools is shown in figure  <dig>  conservative memory usage and efficient c++ implementation enable genomorama to load the sequence and annotations for human chromosome  <dig> substantially faster  than either of the java-based programs on a range of desktop computers.
to assist in experimental design and analysis, genomorama provides dna hybridization-based searches to identify probe binding locations and pcr amplification products.
given a pair of pcr primers, genomorama will display all corresponding pcr amplicons from a target sequence.
both traditional pcr primer and padlock probe  <cit>  queries are supported.
these searches employ a sequence similarity criteria defined by dna melting temperature  <cit> , which allows for non-watson and crick base pairing , and an optional number of exact matching bases at the 3' end of each primer.
all possible combinations of the forward and reverse pcr primers are tested .
in contrast, existing in-silico pcr tools are either inflexible   <cit>  or rely on heuristic similarity measures   <cit> .
genomorama also performs primer prediction by computing all potential forward and reverse pcr primers that satisfy primer length, melting temperature, %g+c and heuristic base composition requirements.
an example of pcr primer based searching, using the b. anthracis specific primers  <cit> , is shown in figure  <dig>  finally, sequence searching  is sensitive to the topology of the target dna molecule  and, as a result, can identify query matches that span the start/stop  of circular genomes.
CONCLUSIONS
genomorama is an easy to use computational tool for a number of genome comparison tasks, including real time display of multiple genomes, high quality output and novel hybridization based sequence searching.
availability and requirements
• project name: genomorama
• project homepage:
• operating systems: os x, windows, linux
• programming language: c++
• license: freely available
• any restrictions on use by non-academics: no
authors' contributions
jg wrote the program and documentation.
mw oversaw the development process.
both authors prepared and approved the manuscript.

 with the rapid growth in the number of sequenced genomes has come a corresponding proliferation of computational tools for viewing, comparing and searching genome sequences and annotations. tools can be divided into two broad categories, database-client and stand-alone. in general, database-client tools offer static visualizations of small sets of predefined genomes, while stand-alone tools allow interactive visualizations of locally stored genomes. stand-alone tools can serve as graphical front ends for displaying the output of locally run calculations. a high level comparison of common features for these stand-alone tools is shown in table and reveals several trends and patterns. almost all of the tools are implemented in an interpreted language. while this provides for cross platform portability, the responsiveness of these applications is poor. while all of the tools can display genome annotations, additional functionalities vary widely between programs. aprograms that use java, tcl/tk and perl are expected to run on any operating system. bcommon file formats include the genbank flat file, embl flat file, nucleic acid sequence file, general feature format and protein table file. a complete list of genome annotation file formats can be found on the genomorama project webpage. cthe graphic output format labeled "printer" indicates direct output to an attached printer. not content with the performance or feature set of existing programs, we wrote genomorama, a stand-alone tool originally developed to assist in computational signature design for bacterial and viral pathogen detection. genomorama allows users designing dna-based hybridization assays, such as pcr or dna probes, to easily identify the regions of a genome targeted by a given assay. it is distinguished from existing tools by dna hybridization-based sequence searching, its rapid execution speed, and ability to read and export a diverse set of common file formats. despite its origins as a viewer for viral and bacterial genomes, genomorama can also visualize large eukaryotic genomes. implementation genomorama is a software program for interactively displaying and analyzing multiple genomes. it provides a powerful yet easy to use interface that leverages the visualization power of modern computers and the substantial bioinformatic infrastructure provided by the ncbi. genomorama is written in portable, highly optimized c++ and comes in three "flavors" that allow it to run natively on modern operating systems: os x, microsoft windows and linux. the motif version allows any x-windows client that supports opengl to remotely run genomorama. executables and source code are freely provided for all flavors.  to visualize and compare annotated genome features at all relevant size scales, genomes are displayed on the computer screen as linear, scale-dependent maps. the user interacts with a map using the mouse, keyboard and scroll bars. semantic zooming is used to display genomic features which occur at a wide range of scales, i.e. ~ bases for a mammalian gene, ~ bases for a pathogenicity island, ~ bases for a bacterial gene, ~ bases for a trna, ~ bases for a transcription factor binding site and for a single nucleotide polymorphism. optional 2d graphs, including %g+c, gc skew and external data sets, can be superimposed on genome maps. publication quality, wysiwyg images can be saved in either gif or postscript formats. genome annotations and sequences are available in a large number of file formats and genomorama can read a substantial subset of these formats, including genbank, european molecular biology laboratory, abstract syntax notation one, protein table and fasta. unlike existing programs, genomorama can read the multi-part gbk, embl and asn. files used to store annotations and sequence for partially assembled sequences for both prokaryotic and eukaryotic organisms. the ability to load multipart annotation files allows access to preliminary annotation information provided by sequencing centers during the whole genome shotgun sequencing of an organism. a screen shot of five contigs and associated sequencing quality scores from the genome sphingopyxis alaskensis rb is shown in figure genomorama can load large genomes. support for large genomes is crucial for visualizing entire eukaryotic chromosomes. a comparison between loading times for genomorama and two java-based visualization tools is shown in figure conservative memory usage and efficient c++ implementation enable genomorama to load the sequence and annotations for human chromosome substantially faster than either of the java-based programs on a range of desktop computers. to assist in experimental design and analysis, genomorama provides dna hybridization-based searches to identify probe binding locations and pcr amplification products. given a pair of pcr primers, genomorama will display all corresponding pcr amplicons from a target sequence. both traditional pcr primer and padlock probe queries are supported. these searches employ a sequence similarity criteria defined by dna melting temperature, which allows for non-watson and crick base pairing, and an optional number of exact matching bases at the 3' end of each primer. all possible combinations of the forward and reverse pcr primers are tested. in contrast, existing in-silico pcr tools are either inflexible or rely on heuristic similarity measures. genomorama also performs primer prediction by computing all potential forward and reverse pcr primers that satisfy primer length, melting temperature, %g+c and heuristic base composition requirements. an example of pcr primer based searching, using the b. anthracis specific primers, is shown in figure finally, sequence searching is sensitive to the topology of the target dna molecule and, as a result, can identify query matches that span the start/stop of circular genomes.  genomorama is an easy to use computational tool for a number of genome comparison tasks, including real time display of multiple genomes, high quality output and novel hybridization based sequence searching. availability and requirements • project name: genomorama • project homepage: • operating systems: os x, windows, linux • programming language: c++ • license: freely available • any restrictions on use by non-academics: no authors' contributions jg wrote the program and documentation. mw oversaw the development process. both authors prepared and approved the manuscript. 
to assist in these tasks, we present genomorama, a software program for interactively displaying multiple genomes and identifying potential dna hybridization sites for assay design. useful features of genomorama include genome search by dna hybridization, efficient multi-scale display and manipulation of multiple genomes, support for many genome file types and the ability to search for and retrieve data from the national center for biotechnology information entrez server. genomorama provides an efficient computational platform for visualizing and analyzing multiple genomes.
 the ability to visualize genomic features and design experimental assays that can target specific regions of a genome is essential for modern biology. to assist in these tasks, we present genomorama, a software program for interactively displaying multiple genomes and identifying potential dna hybridization sites for assay design.  useful features of genomorama include genome search by dna hybridization, efficient multi-scale display and manipulation of multiple genomes, support for many genome file types and the ability to search for and retrieve data from the national center for biotechnology information entrez server.  genomorama provides an efficient computational platform for visualizing and analyzing multiple genomes. 