Genomorama

Multi-scale, Multi-genome, Multi-platform Visualization and Analysis
Version 1.55
Last Updated July 17, 2007
J. D. Gans
Los Alamos National Lab, Bioscience Division

Overview

"Yet another genome viewer?"

Features

Getting started

OSX
Microsoft Windows

Linux

Reporting a problem/Requesting a feature
Known problems

Annotation data

Supported file formats
Loading data from files
Loading data from NCBI
Exporting sequence and annotation data
Annotation resources on the web
Annotation shape and color key

Genome navigation

Keyboard controls
Mouse controls
Selection
Genome roulette
Genome display (gene or size-centric)
Displaying annotation details
Magnifying annotations
Adding and removing genomes

Genome analysis and manipulation

Base content
Melting profile
Genome plot
Sequence complement

Genome searching

Annotation based queries

gi
Locus name/tag
Annotation text

Sequence based queries

DNA substring
DNA hybridization

Probe hybridization
PCR primer hybridization

Genome editing

Add genomes
Delete genomes

Add annotations
Delete annotations
Editing and creating annotations
Picking primers

Appearance customization

Text Font
Colors
Number of genomes to display
Hiding a genome
Genome display order

Making pictures

Supported export file formats
printing

Exporting sequence and annotations

DNA sequence
Amino acid sequence
Exported annotation file formats

Overview

Genomorama is a software program for interactively displaying multiple genomes. In this context, a genome refers to DNA sequence and an (optional) collection of annotations (indicating which DNA sub-sequences correspond to genes, RNAs, proteins etc.). Genomorama was designed to assist in comparative genomics, sequence comparison and sequence analysis. To this end, Genomorama provides a powerful yet easy to use interface that leverages the visualization power of modern computers (via OpenGL) and the substantial bioinformatic infrastructure provided by the NCBI (via the NCBI C toolkit). Genomorama is written in portable, highly optimized C++ and comes in three "flavors" that allow it to run natively on (most) modern operating systems: OS X (using Carbon), Microsoft Windows (using MFC) and Linux (using Motif). Executables and source code are freely provided for all flavors.

By now, you're probably wondering: "Does the world really need another genome viewer?". Predictably, my answer is "yes". Here's why:

High performance has not been sacrificed on the altar of portability

OpenGL graphics take advantage of the video-game optimized graphics cards available in most desktop and laptop computers.
C++ allows transparent and complete utilization of system resources (like memory).
Native windowing toolkits (Carbon, MFC and Motif) for every operating system facilitate responsiveness and ease of use.
A stand-alone, self-contained executable frees Genomorama from dependence on third party applications.
Source code for all platforms is freely available.

An attractive, full featured user interface

Genomorama presents a clean, uncluttered user interface.
Multi-scale rendering ("Semantic Zooming") displays relevant details while maintaining readability.
Use a keyboard or a mouse to efficiently zoom, pan and explore genomes of arbitrary size.
Attractive WYSIWYG Postscript and GIF output formats yield publication quality images.

Useful features to aid genome analysis

In addition to the standard searching options (like query by sequence and gene name), Genomorama offers "forward and reverse" DNA hybridization based searches.

Provide a pair of PCR primers, and Genomorama will output the amplicons.
Provide a hybridization probe and Genomorama will find binding sites.
Provide a pair of Padlock probes and Genomorama will identify binding locations
Provide a set of PCR primer criteria (length, melting temperature, base composition, etc.) and Genomorama will find PCR primers.

Genomorama can display and search an arbitrary number of genomes (limited only by computer memory).
Harness the power of the NCBI toolkit to directly access and search the NCBI Entrez database.
Compute melting profile, in addition to traditional base composition plots (i.e. %G+C, %A+T, etc).

Here is a brief comparison with other freely available "Stand-alone" Genome viewers (if you find an error in any of this information or omission, please let me know!):

Program	Platforms	Source code available	Input formats	Graphic output formats	Circular view	Linear view	Real time navigation	Multiple genomes	Annotation editing and creation	Annotation searching	Sequence searching
Genomorama	OS X, Windows, Linux	√	EMBL, GBK, ASN.1, FASTA, PTT	PS, GIF		√	√	√	√	√	√
Artemis	Java	√	EMBL, GBK, FASTA, GFF	JPG, PNG		√	√	√ (via ACT)	√	√	√
Sockeye	Java		EMBL (via server), GFF	JPG		√	√	√
Apollo	Java	√	GAME XML, GFF, GBK, EMBL, FASTA	PS		√	√		√	√	√
Argo	Java		GFF, GBK, GENSCAN, BLAST	Printer		√	√	√ (2)	√	√	√
IGB	Java	√	GFF, FASTA, PSL, DAS	Printer		√	√		√	√	√
GeneViTo	Java		PTT+FFN+FNA	JPG	√	√			√	√	√
CGView	Java	√	PTT, XML	PNG, JPG, SVG	√
GenoMap	Tcl/Tk	√	GRS	PS	√
Genome2D	Windows		GBK, FASTA, GLIMMER, PARADOX	Printer, WMF, BMP		√	√	√	√	√	√
GenomeComp	Perl/Tk	√	EMBL, GBK, FASTA	PS		√	√	√ (2)		√
GRS	Linux, Dec, Solaris	√	GRS	Printer	√	√		√		√
Mauve	Java	√	GBK, FASTA, SEQ	PNG, JPG		√	√	√
GATA	Java	√	GFF	PNG		√	√	√(2)
GenomeViz	Tcl/Tk/Perl (no Windows)	√	tab delimited	PS	√		√	√		√
GenomePlot	Tcl/Tk/Perl	√	tab delimited	PS, GIF, TIFF, JPG	√	√	√
Bluejay	Java		XML	Printer, SVG	√		√		√
SeqVISTA	Java	√	EMBL, FASTA	JPG		√	√	√	√		√
DNAvis	Windows, Linux		GFF, FASTA			√	√	√
AlignScope	Java		PTT + (BLAST \| GAME)			√	√	√ (2)
Genome Workbench	OS X, Windows, Linux	√	ASN.1, XML, FASTA, GFF			√	√		√	√	√

For completeness, here is a list of database-driven genome visualization tools:

Program	Platforms	Source code available	Graphic output formats	Circular view	Linear view	Real time navigation	Multiple genomes	Annotation editing and creation	Annotation searching	Sequence searching
Microbial Genome Viewer	Browser-SVG	√	Printer, SVG	√	√
cMap	Java	√	Printer		√	√	√		√
ERGO Light	Browser-HTML		Printer		√				√
tair	Brower-Java		Printer		√					√
Jena Genome Viewer	Browser-HTML		PNG, PDF, PS	√			√		√	√
Lightweight Genome Viewer	Browser-HTML	√	Printer		√
ChromoWheel	Browser-SVG		Printer, SVG		√
GenDB	Perl/Gtk	√	PNG	√	√	√		√	√
BioVis	Browser-SVG (no Unix)	√	Printer, SVG		√	√	√		√
Vista	Java	√	PDF, JPG, GIF		√	√	√
UCSC Genome Browser	Browser-HTML	√	PDF, PS		√		√	√

Graphic format key:

Vector formats (variable resolution)	Bitmap formats (fixed resolution)
SVG (Scalable Vector Graphics)	JPG (jpeg)
PS (Postscript)	PNG (Portable Network Graphics)
PDF (Portable Document Format)	GIF (Graphics Interchange Format)
WMF (Windows MetaFile)	BMP (Windows Bitmap)

Printer = "Output to a printer"

How to get started using Genomorama.

1) Download Genomorama.

Windows	binary^a	source^b
OS X	binary (powerPC)^a binary(Intel)^a	source^b (for XCode 1.1)
Linux (Unix)		source^b

a = No installation is required. Binary is self contained -- just unzip/untar and run!
b = The NCBI toolkit must be installed before compiling Genomorama. Documentation is included with the source distributions.

If you need to compile Genomorama, please read these build instructions.

2) Run Genomorama, either by double clicking on the Genomorama executable [OSX and win32] or typing ./genomorama [Linux] or genomorama [win32] on the command line.
The win32 and Motif versions support opening multiple files from the command line (wild cards are allowed), while the OSX version supports drag-and-drop.

Here is sample genome annotation file (in binary ASN.1 format) from the good people at NCBI.

Reporting a problem/Requesting a feature

Please send all correspondence here.

Known Problems

Genomorama can fail when downloading large genome files (like human chromosomes). If this happens, please download the genome file directly from the NCBI webserver and save the file to disk. When downloading a large genome file, please choose the "Genbank(full)" display option on the NCBI web page. After the file has been saved to disk, load it into Genomorama (using "File | Open ..." on the Genomorama menu bar).

To improve download reliability (and improve performance), only annotations for large genomes will be downloaded from the NCBI webserver. If you need sequence data, please download directly from the NCBI to your local hard disk.

Annotation data

There are a number of common genome annotation and sequence file formats. Here is the current status of supported formats:

NCBI	ASN.1	.asn, .val	Both ASCII and binary formats are supported
GenBank Flat File (US)	GBK	*.gbk	Supported
GenBank Flat File (Europe/EMBL)	EMBL	*.embl	Supported
Nucleic acid sequence	FASTA	.ffn, .fna	Supported; Each sequence in a file is assumed to correspond to a gene
Protein Table File	PTT	*.ptt	Supported
Amino acid sequence	FASTA	*.faa	Supported (export only)
Genome Annotation Markup Elements	GAME XML		Not supported
GENSCAN (gene predicition) output file	GENSCAN		Not supported
GLIMMER (gene prediction) output file	GLIMMER		Not supported
Extensible Markup Language	XML		Not supported
tab delimited (application specific)	tab delimited		Not supported
GRS input file	GRS		Not supported
General Feature Format	GFF		Not supported
Distributed Annotation System	DAS		Not supported
BLAT output	PSL		Not supported
Gene Transfer Format	GTF		Not supported
DNASTAR SEQ Format	SEQ		Not supported

Note that the file extensions are provided here for completeness only -- Genomorama determines file type automatically.

Loading data from files

There are four ways to read data files stored on your local system:
1) Interactive file loading. Go to "File | Open ..." and choose file(s) to open. Multiple file selection is supported for Windows and OS X.
2) Import annotations into an existing genome. Genome annotations in either GBK, ASN or PTT file formats may be
imported into an existing genome by selecting "Genome | Import Annotation..." on the menu bar.
3) Command line file loading. Specify any number of data files to open by appending the filenames on the command line [Not supported on OS X].
4) The OS X version of Genomorama supports drag and drop file loading.

Q: "How do I view an annotated genome when the sequence is stored in a fasta file but the annotations are stored in a PTT file?"

A: First load the fasta file (using "File | Open ..." on the menu bar). This will create a "genome" record by concatinating all sequences in the fasta file. Each sequence will be annotated as a gene. Then, selected the destination genome and import the PTT file (using "Genome | Import Annotation ..." on the menu bar). All of the annotations stored in the PTT file will be added to the selected genome. Finally, remove the default "gene" annotations that were created for each fasta sequence by selecting (i.e. left mouse click) the offending annotation and choosing "Genome | Delete Annotation" from the menu bar.

Loading data from NCBI

Annotated genomes can be downloaded from the NCBI Entrez web server.
1) Go to "File | Download ..."
2) Select the search key to use when querying the Entrez system
3) Enter a search string. The "User Defined (Entrez)" search syntax is defined here.

Please note that Genomorama can have trouble downloading very large genomes (like human chromosome 1) -- bacterial and viral genomes should not be a problem. If you wish to display large eukaryotic sequences, I recommend first downloading the genome with a web browser and saving the genome to a local disk in "GenBank(full)" format (saving in ASN.1 format will not download the sequence data).

To improve download reliability (and improve performance), only annotations for large genomes will be downloaded from the NCBI webserver. When the genome is large enough that sequence data will not be downloaded, Genomorama will display an warning message and all nucleotides will be displayed at unknown bases (i.e. 'N'). If you need sequence data, please download directly from the NCBI to your local hard disk (please see the "How to load large genomes" question below).

There are a number of Genome annotation resources available on the web, including NCBI and EMBL.

Q: "How do I load large (i.e. eukaryotic) genomes into Genomorama?"

A: Please note that when downloading genome annotation files for large sequences (i.e. human, mouse, etc.), steps must be taken to insure that the file actually contains sequence data. For instance, seaching for human chromosome 1 (accession NC_000001) in the Entrez nucleotide database yeilds a result that does not contain any sequence or detailed annotation information! If you wish to download large genomes into Genomorama, please use one of the following proceedures:

Download the genome of interest using Genomorama's built-in download feature. For example, to download human chromosome 1, select "File | Download ..." from the menu bar and then select "taxa name" as the "Search by" option. Type the search string "homo sapiens" into the search box and press "Search". This will display a list of all available human chromosomes and mitochondrial sequences. Select the desired entry and press "Load" to download and display the selected genome.
Download the genome of interest directly from NCBI -- making sure to request all annotation and sequence data. By default, searching for NC_000001 in the Entrez nucleotide database yeilds a result that does not contain sequence or detailed annotation information (it contains high level annotation information). To retrive sequence and annotation information, select the link at the top of the page that says "Click here to see all features and the sequence of this contig record." This link adds the "view=gbwithparts" argument to html address and will start the (potentially lengthy) download of the entire genome sequence and all annotations. Set the "Send to" option to "File" to save the genome to disk. After the download is complete, this file can be read by Genomorama to display the genome sequence and annotations.

Exporting sequence and annotation data

Genomorama can export both sequence and annotations in a number of formats. These formats can be: sequence only (protein or DNA FASTA files), annotation only (PTT files) or both sequence and annotation (GBK files). Please note that the PTT format only supports a single genome per file, while all other formats can store multiple genomes per file.

Annotation shape and color key

Genomorama uses a variety of colors and shapes to visually represent annotation and sequence information. The following images illustrate Genomoramas shapes and default colors.

Image and color key

1) Annotations shown as arrows apply to a particular DNA coding strand: right pointing arrows = plus strand and left pointing arrows = minus strand.
2) A single protein coding sequence (CDS) is only displayed when the extent of the CDS differs from that of the parent gene.
3) A gene that contain multiple coding sequences is displayed as an indented arrow.
4) Miscellaneous annotations are shown as blue arrows without a text lable.
5) Intergenic space is shown as a grey box.

Matching sequence on the plus strand

The sequence shown in red indicates a successful match of a query sequence to sequence on the plus strand of the target genome.
Matching sequnce on the minus strand

The sequence shown in blue indicates a successful match of a query sequence to sequence on the minus strand of the target genome.

Genome navigation

Our goal is to provide an intuitive and informative way to explore genomic data. Since genomes contain multiple levels of detail, Genomorama employs multi-scale visualization: the picture you see depends on the current scale. This is the same approach used by cartographers when constructing maps. Only features appropriate to the scale of the map are displayed. For example, if reasonably sized map of the world attempted to show city streets, it would be totally illegible.

Display width (in bases)	Displayed objects	Example
Gene-centric Genome Display
width > 15000	Genes/Pseudo genes/RNA
Annotation size-centric Genome Display
width > 15000	Annotations greater than the length (i.e. size) of the median genome annotation

15000 > width > 70	All annotations
width < 70	Sequence

The following keyboard commands control the appearance and function of Genomorama:

Command	Windows	OS X	Linux
Scroll left	Left arrow
Scroll right	Right Arrow
Scroll up	Page Up
Scroll down	Page Down
Zoom in	Up Arrow
Zoom out	Down Arrow
Fit genome to window and center at base 0	Ctrl+r	Command+r	Ctrl+r
Search dialog	Ctrl+f	Command+f	Ctrl+f
Search again	Ctrl+g, F3	Command+g	Ctrl+g, F3
Edit Annotation Dialog	Ctrl+e
Select all genomes	Ctrl+a	Command+a	Ctrl+a
Clear all selections	Esc
Complement selected genome	Ctrl+i	Command+i	Ctrl+i
Shift selected genomes up	Shift+Up Arrow
Shift selected genomes down	Shift+Down Arrow
Increase the number of genomes per page	+
Decrease the number of genomes per page	-
Jump to base number 'N' (just like the vi text editor)	'N' Shift+g
Magnify the annotation currently under the pointer	Ctrl+m	Command+m	Ctrl+m
Quit the program	Ctrl+q	Command+q	Ctrl+q

The following Mouse/Pointer actions control the appearance and function of Genomorama:

Command	Windows and Linux	OS X^a
Scroll Left	Left Button click and drag	[Left] Button click and drag
Scroll Right	Left Button click and drag	[Left] Button click and drag
Scroll All Genomes (Left/Right/Up/Down)	Middle button click and drag	Middle button click and drag
Zoom In	Right button click and drag, Wheel	Right button click and drag, Wheel
Zoom out	Right button click and drag, Wheel	Right button click and drag, Wheel
Select genome	Left button click	[Left] Button click
Toggle select multiple genomes	Ctrl+Left button click	Command + [Left] Button click
Genome information	Left button double click	[Left] Button double click
Annotation information	Left button double click	[Left] Button double click
Display sequence: Set first base	Shift + Left button click	Shift + [Left] Button click
Display sequence: Set last base	Shift + Left button click	Shift + [Left] Button click

a = Under OS X, a three button wheel mouse is recommend

Genome roulette

To allow genomes to spin freely in the display window, select "View | Momentum". Start things spinning by dragging a genome with the left mouse button. Are you feeling lucky?

Selection

Both genomes and genome annotations are selectable. Selection is used to specify the target of various actions in Genomorama. For instance; to delete or complement a genome requires that it first be selected, to display a dialog box with the sequence of a gene in FASTA format requires that the gene first be selected, etc. Selection is accomplished by clicking on the desired object with the [left] mouse button. Multiple objects can be selected by repeating this procedure while holding down the Ctrl [Windows/Linux] or Command [OS X] button.

When a genome is selected, it will be surrounded with a dotted line.
When an annotation is selected, the color will change to the predefined selection color (yellow by default). In addition, a brief description of the annotation (if available) will be displayed on the screen.

All selections can be "turned off" by pressing the "Esc" key.
All genomes can be selected by pressing Ctrl+A [Windows/Linux] or Command+A [OS X].

Genome display

To change between the "Gene-centric" and the "Size-centric" representations, select "View | Size centric" or "View | Gene centric" on the menu bar.

Displaying annotation details

To display all available information about a particular annotation, double click on the annotation with the [left] mouse button.
A dialog box will appear containing information about the selected annotation.

Magnifying annotations

To compenstate of the loss of legibility when genome annotations become crowded on the screen (either due to the zoom level or a large number of overlapping annotations), Genomorama can "magnify" the annotation that is currently under the mouse pointer. Magnification can be enabled via the menu bar ("view | magnify") or the keyboard (Ctrl+M or Command+M). The figure below shows an example of the magnification effect applied to Human chromosome 22.

A "magnified" gene from human chromosome 22

A "magnified" gene from human chromosome 22

Adding and removing genomes

Additional genomes can be added to the Genomorama display by loading the new genomes from disk or downloading from the NCBI.
Existing genomes can be removed from the display by first selecting and then deleting (via "Edit | Delete Genome" on the menu bar).

Genome analysis and manipulation

Base content

Genomorama can compute the following quantities:

%G+C =	(G_f + C_f)/(A_f +T_f + G_f + C_f + N_f)
%A+T =	(A_f + T_f)/(A_f +T_f + G_f + C_f + N_f)
GC Skew =	(G_f - C_f)/(G_f + C_f)
AT Skew =	(A_f - T_f)/(A_f + T_f)
Keto Skew =	(G_f + T_f - A_f - C_f)/(A_f +T_f + G_f + C_f + N_f)
Purine Skew =	(G_f - T_f + A_f - C_f)/(A_f +T_f + G_f + C_f + N_f)

where A_f, T_f, C_f, G_f, and N_f are the windowed frequencies of the bases A,T, C, G and N.

To show a content plot, first select the genomes of interest and then choose "Genome | Plot | <content>" on the menu bar (where <content> is "%G+C", "%A+T", "GC Skew", "AT Skew", "Purine Skew" or "Keto Skew"). The content plot will appear overlaid on the selected genomes. The window size for computing content plots can be adjusted via the options dialog (i.e. "View | Options ..." on the menu bar).

Values are displayed in the status bar [Windows and Linux] or title bar [OS X] for the base at the current pointer location.

Melting profile

The melting profile is defined by computing the hybridization temperature (T_m) for a sliding window of DNA bases.

To show the melting profile, first select the genomes of interest and then choose "Genome | Tm" on the menu bar. The T_m plot will appear overlaid on the selected genomes. The hybridization temperature is a function of window size, salt concentration [Na+] and DNA concentration [strand]. All three of these values can be adjusted via the options dialog (i.e."View | Options ..." on the menu bar). Values of T_m are displayed in the status bar [Windows and Linux] or title bar [OS X] for the base at the current pointer location.

DNA hybridization is computed using the nearest-neighbor method. Parameters are taken from Owczary et. al., Biopoly 44: 217-239, 1997, Allawi and SantaLucia, Biochemistry 36: 10581-10594, 1997 and SantaLucia, PNAS 95: 1460-1465. The salt and DNA strand concentration parameters have been choosen to closely match Primer3 T_m predictions.

The code that computes the melting temperature is original to Genomorama and is contained in the files nuc_cruc.cpp and nuc_cruc.h.

Genome plot

For a genome with N bases, Genomorama will display an arbitrary function of the form f(i), where i is an integer in the range [0, N-1]. To load a genome plot, choose "File | Load Genome Plot..." on the menu bar and select the file contains the plot data. The numeric genome plot values are displayed in the status bar [Windows and Linux] or title bar [OS X] for the base at the current pointer location. To toggle the display of a genome plot, select "Genome | Plot | User" on the menu bar.

The genome plot file is an ASCII test file and must have the following format:

> header_string_1
a₀ f₁(a₀)
a₁ f₁(a₁)
a₂ f₁(a₂)
...
> header_string_2
b₀ f₂(b₀)
b₁ f₂(b₁)
b₂ f₂(b₂)
...
where the header_string matches a genome identifier string (i.e. GenBank accession, gi value, etc). As shown in this example, multiple plots can be loaded from the same file.

Sequence complement

By default, Genomorama displays all genes, annotations and sequence using the coding strand used in the annotation file. To switch a genomes representation to the complement strand, first select the genome and then choose "Genome | Complement" on the menu bar. If the complement of a genome is performed twice, the original representation is restored.

Genome searching

Genomorama offers a number of ways to search a genome: annotation, label, DNA sequence and DNA hybridization.
Note that all currently loaded genomes are searched, independent of currently selected genomes. Any genome that contain a match becomes selected.

If Genomorama is *not* displaying sequence, then annotations that are matched are sequentially selected (the "find next" button jumps to the next matching annotation). If Genomorama is displaying sequence, then *all* annotations that are matched are simultaneously selected.

Query Target	Query String	Notes
Annotation Keyword(s)	one or more text strings	Keyword searches are case insensitive and do not depend on the order of query strings.
gi	number	Compare input number against the gi of all loaded annotations.
Locus Name/Tag	string	Compare input string against both locus name and tag of all loaded annotations.
DNA sequence string	string (characters can be A, T, G or C)	Sequence matching is case insensitive. Both positive and negative strands are searched. Matches are allowed to wrap around circular.DNA molecules (i.e. plasmids and circular genomes). Probe lengths must be greater than 10 and less than 100 bases (values set a compile time). Primer lengths must be greater than 10 and less than 100 bases (values set a compile time). Gaps are not allowed. The optimal sub-string match for hybridization searching is determined using dynamic programming. Only exact matches are reported for DNA sequence string searches. The default salt and DNA strand concentration parameters have been choosen to closely match Primer3 T_m predictions.
Probe hybridization	string (characters can be A, T, G or C)
PCR hybridization/extension	pair of strings (characters can be A, T, G or C)

Genome Editing

Add genomes

To add one or more genomes to the display, either load from disk or download from NCBI.

Delete genomes

To delete one or more selected genomes, choose "Edit | Delete Genome".

Add annotations

Genomorama allows the creation of new annotation corresponding to sequence regions returned by a genome search.
To add annotation:

Search by DNA sequence string, probe hybridization or PCR hybridization/extension
If matches are found, press the "Annotate" button to add an annotation for each match

Delete annotations

To deleted all selected annotations, choose "Genome | Delete Annotation".

Editing and creating annotations

Genomorama provide a single dialog box for the manual creatation and editing of genome annotations.

To create a new annotations, select the target genome and choose "Genome | Edit annotation ..." from the menu bar.
To edit an existing annotation, select the target annotation and choose "Genome | Edit annotation ..." from the menu bar.

In both cases, the edit annotation dialog box (see below) will appear and allow you to enter annotation attributes. If you are
creating a new annotation (and have not selected an existing annotation) then the fields of this dialog box will be empty.

Annotation editor

The boundaries of the annotation are specified by the "Range:" string -- which has the format "start..stop" (inclusive, starting from 0).
If the annotation has multiple segments (i.e. multiple coding regions separated by introns) then the Range defines a
comma delimited list of segment boundaries; "start1..stop1, start2..stop2, start3..stop3, ...".

The only required information is the Range.

Picking primers

Genomorama can annotate a genome with allowed forward and reverse PCR primers. To add primers, first select the genome(s) and then bring up the Primer dialog by selecting "Edit | Primers | Pick Primers ..." on the menu bar. The primer dialog displays a number of options for defining a valid PCR primer (i.e. length, melting temperature, hairpin/dimer temperature, %G+C, etc.).
Please note that:

Picking primers can take a while for large genomes.
Primer annotations are small (~20 bases) and may not be visable without zooming in.
To avoid primer hetero-dimers, one should use potential forward and reverse primers as search keys and search the selected genome(s). The search output will contain the hetero-dimer melting temperature.

Primer predictions for the current genome can be deleted by choosing "Edit | Primers | Delete Primers" on the menu bar.

The source code that predicts primer binding sites is original to Genomorama and is contained in the file annotation_primer.cpp.

Appearance Customization

Text Font:
Font size can be changed with the options dialog via "View | Options ..." on the menu bar.
The font typeface can not currently be changed since the font is stored internally to achieve cross-platform portability. Multiple fonts may be added in the future.

Colors:
There is a single background color that can be adjusted via "Color | Background ..." on the menu bar.
Colors for genome specific objects (like annotations, text and selected annotation) are adjusted by first selecting the genomes to modify and then changing the appropriate color using "Color" on the menu bar. The "Custom" color options overrides the color of all currently selected annotations.

Here are the default color settings:

Selected annotations	Yellow
Background	White
Text	Black
Gene	Red
Pseudo-gene	Pink
CDS	Green
Misc annotations	Blue
RNA	Black
Intergenic space	Grey

Number of genomes to display:
The number of genomes to display at the same time (without scrolling) is incremented by pressing the "+" key (or choosing "Genome | Show | One more" on the menu bar) and decremented by pressing the "-" key (or choosing "Genome | Show | One less" on the menu bar).

Hiding a genome:
Selected genomes are hidden by choosing "Genome | Hide" on the menu bar.
All hidden genomes are shown by choosing "Genome | Unhide" on the menu bar.

Genome display order:
The order in which a selected genome appears in the Genomorama window can be changed by moving a selected genome up (using "Genome | Move | Up" on the menu bar) or down (using "Genome | Move | Down" on the menu bar). The order of genomes is periodic, so moving the bottom genome down "wraps" the genome around to the top. Similarly, moving the top genome up "wraps" the genome around to the bottom.

Making pictures

Genomorama offers WYSIWYG ("What You See Is What You Get") output and currently supports two export file formats: Postscript and GIF. The postscript format offers high resolution and is compatible with a number of programs including Adobe Illustrator ^tm and Microsoft Powerpoint ^tm. The GIF format offers small file size, suitable for web pages.

To export the currently displayed Genomorama image, choose "File | Export ..." on the menu bar.

Direct printing from Genomorama is not currently supported. Use a third party application (like Illustrator or PowerPoint) to print a Genomorama-generated Postscript file for best results.

Please note the following when editing or converting Postscript files:

To maintain image quality when converting a Postscript to PDF file in Adobe Acrobat, turn off the "Smooth line art" option in "Edit | Preferences | Smoothing".
To maintain image quality when editing Postscript files in Adobe Illustrator, turn off the "Anti-aliased Artwork" option in the General Preferences dialog.

Exporting sequence and annotations

For sub-regions of a genome, Genomorama can display both DNA sequence and corresponding amino acid sequences in FASTA format. Sequences are displayed as text is a dialog box which can be copied into other applications.

To display the DNA sequence of a selected gene, choose "Sequence | FASTA | DNA" on the menu bar.
To display the amino acid sequence of a selected gene, choose "Sequence | FASTA | Protein" on the menu bar.
Annotations that do not encode proteins will be translated in all six reading frames (three from the positive strand and three from the negative strand).

To display the DNA and amino acid sequence of an arbitrary fragment of DNA:

Select the first base of the fragment by clicking the [left] button of the mouse while holding down the shift key.
Select the second base of the fragment by clicking the [left] button of the mouse while holding down the shift key.
A dialog box will appear containing the selected sequence.
If the fragment overlaps a protein (or proteins), then the overlapping protein regions define the amino acid reading frame.
Otherwise, amino acid sequences for all six reading frames are displayed.

Exported annotation file formats

Genomorama can export entire genomes (which allows changes in genome annotation to be saved to disk).

Currently supported file formats for export include: FASTA (entire genome, DNA or amino acid sequences), GBK (Genbank format) and PTT (protein table).

To export the currently selected genomes, select "File | Export | Genomes" on the menu bar. This will bring up the export genome(s) dialog box and
allow you to select which annotations features to export and the export format.

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