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


Table of contents


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:
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
binarya
sourceb
OS X
binary (powerPC)a
binary(Intel)a
sourceb (for XCode 1.1)
Linux (Unix)

sourceb
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

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:
  1. 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.
  2. 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
Genes

Annotation size-centric Genome Display

width > 15000 Annotations greater than the length (i.e. size) of
the median genome annotation
Large size view

15000 > width > 70
All annotations Gene and misc annotation scale
width < 70
Sequence
Sequence scale


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 Xa
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

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 =
(Gf + Cf)/(Af +Tf + Gf + Cf + Nf)
%A+T =
(Af + Tf)/(Af +Tf + Gf + Cf + Nf)
GC Skew =
(Gf - Cf)/(Gf + Cf)
AT Skew =
(Af - Tf)/(Af + Tf)
Keto Skew =
(Gf + Tf - Af - Cf)/(Af +Tf + Gf + Cf + Nf)
Purine Skew =
(Gf - Tf + Af - Cf)/(Af +Tf + Gf + Cf + Nf)

where Af, Tf, Cf, Gf, and Nf 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 (Tm) 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 Tm 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 Tm 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 Tm 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 Tm 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:
  1. Search by DNA sequence string, probe hybridization or PCR hybridization/extension
  2. 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:
  1. Picking primers can take a while for large genomes.
  2. Primer annotations are small (~20 bases) and may not be visable without zooming in.
  3. 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:

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:
  1. Select the first base of the fragment by clicking the [left] button of the mouse while holding down the shift key.
  2. Select the second base of the fragment by clicking the [left] button of the mouse while holding down the shift key.
  3. A dialog box will appear containing the selected sequence.
  4. If the fragment overlaps a protein (or proteins), then the overlapping protein regions define the amino acid reading frame.
  5. 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.



Los Alamos National Lab
Operated by the Los Alamos National Security, LLC
for the National Nuclear Security Administration,
of the US Department of Energy.
Copyright © 2005 LANSLLC | Disclaimer/Privacy