Desktop Sequence Analysis Packages

In response to many requests from the Penn community, the Bioinformatics Core facility has negotiated licenses and set up a centralized key server for a number of desktop sequence analysis packages. This enables us to provide these packages to Penn Scientists at a fraction of the cost for static licenses. An additonal advantage is that the packages can be run on multiple computers without the need for a hardware licensing device or key. Following are the software packages currently available.

MacVector 10: Provides a comprehensive set of sequence analysis tools. "MacVector provides sequence editing, PCR primer analysis, Internet database searches, protein analysis, and a wide variety of other functions. View the results of any analysis function in graphical or text format. Assemble consensus sequences for your sequencing projects with AssemblyLIGN, MacVector’s contig assembly module." (Macvector)

AccelrysGene 2.5: Accelrys has decided to "end-of-life" this software product. They will continue to support the software through the end of our maintenance agreement, March '08. It is not clear whether we will be able to maintain access past that point. The functionality of AccelrysGene is a subset of other programs in the subscription. (Accelrys)

Sequencher 4.8: (Mac and PC) "The tool of choice for contig assembly, sequence analysis and SNP detection. Imports NCBI GenBank sequences and annotation and provides numerous functions for batch sample handling." Live technical support (http://genecodes.com/contact) and tutorials (http://genecodes.com/sequencher/tutorials.html) available to all subscribers.

Lasergene 7.2: "Lasergene is a comprehensive suite of easy-to-use sequence analysis software for Windows and Macintosh" (DNAStar). This product runs on both Mac and PC and the developers are committed to maintaining releases for both platforms. This is a full featured package and includes all the modules available for Lasergene7.

VectorNTI Advance: "Our comprehensive set of data analysis and management tools are integrated in a single analytical environment. This integration allows you to focus on your research objectives and avoid the distractions of data manipulation and reformatting. Simplify your research planning and save analysis time using the five integrated modules of Vector NTI Advance™" (InVitrogen). Vector NTI runs on both PC and MacOSX 10.2 and 10.3. It does not run on MacOSX Tiger (10.4). Vector NTI is now a free product for academic scientists. In Vitrogen sees it as a marketing tool for their molecular biology products which seems like a win win situation to us. If you are planning on using only Vector NTI and not any of the other tools, do not subscribe to the sequence tools as Vector NTI is available at no cost at the InVitrogen User Community web site.

Fees: Rather than passing on to users a license to individual packages, we have decided to provide all four packages to investigators for an annual subscription to sequence analysis desktop software provided by the Bioinformatics Core. The cost of this subscription is $300 / year / lab for installation onto two computers. Installation on more than two computers costs an additional $50 / computer / year. This is a small fraction of the cost of purchasing any one of these packages and has the added advantage that the programs can be run on multiple computers at the same time without worrying about hardware dongles or keys.

Our commitment: The Bioinformatics Core is committed to maintaining the license servers with the latest version of the software and enough licenses to satisify the needs of the Penn community.

Signing Up: You can sign up for this software by filling in this form. If you have any questions regarding this service, please email the bioinformatics core and we will get back to you promptly.

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