Genomorama: Genome Visualization 1.4 review

Genomorama: Genome Visualization is a multi-scale, multi-genome, multi-platform visualization and analysis program

License: Freely Distributable File size: 193K Developer: J. D. Gans

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Genomorama: Genome Visualization is a multi-scale, multi-genome, multi-platform visualization and analysis program. It 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.

Here are some key features of "Genomorama Genome Visualization":
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 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.
Novel 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).

What's New in This Release:
Added a selection guide for picking nucleotide sequence to display and translate into amino acids.
Fixed bug that caused clipping rectange to overlap neighbooring genomes.
Fixed bug in sequence selection (a selection that ended on the last base of the genome caused an infinite loop!).
Added a new annotation key to the GBK file parser -- "signature".
Fixed bug when inverting genome plot.
Fixed bug when parsing genome files with no genomes.
Fixed bug when clipping multiple genomes.
No longer throw an error when the GIF color table is exhausted -- use the closest color available instead.
Added the ability to import genome annotations from Protein Translation Table (ptt) files.
Fixed a bug in exact match DNA searching.
Added the ability to import annotations from any genome file that contains annotation (i.e. asn, gbk, embl, ptt). As with loading files, the file type is autodetected!
Fixed a import bug in the GBK file format (assigning GI values)
Added a horizontal scroll bar for scrolling all genomes left and right
Added a vertical scroll bar for zooming all genomes
Added the ability to export genome data (i.e. sequence and annotation) to the following formats: Fasta (protein and DNA), PTT and GBK
Fixed line numbers on GBK parse error messages.
Fixed lack of intergenic space for certain annotation combinations.
Fixed bug in the translation guide rendering (that could cause infinite loop under certain conditions).
Pressing the esc key now cancels any pending translation.
Added the ability to load multiple genomes from a single ASN file.
Fixed the rendering of *multiple* annotations that all overlap the origin.
Added search by genome name.
Modifed the EMBL parser to handle Artemis files.
Fixed bug in searching for Padlock/MOL-PCR probes
Added an annotation editor