Coming to a Computer Near You -- Double Twist Functional Genomics Tools

The company formerly known as Pangea (Oakland, CA) has a new name, a new look, and a new concept in providing tools for researchers. The company, now known as DoubleTwist, is providing free on-line access to significant parts of its bioinformatics software collection. Working with its scientific advisory team, led by Douglas Brutlag (Stanford University), DoubleTwist has produced a well-crafted and tested set of research agents that provides significant time savings to gene jockies, whether you're a novice or an old hand. What follows is a summary of a presentation on DoubleTwist given by Brutlag to the American Society of Cell Biology annual meeting in last month.

What Is DoubleTwist.com?
How Does DoubleTwist.com Work?
And There's More
View from the Lab Bench
Ready To Go

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What Is DoubleTwist.com? (Back to Top)
DoubleTwist.com is a web portal for life scientists that integrates powerful and sophisticated genetic research tools and data through an easy-to-use interface. It links the user, through the use of a query, to multiple databases, both public and proprietary, and provides a variety of analyses through a set of automated agents that perform repetitive tasks, search the literature, and report updates to you daily.

DoubleTwist.com is designed for the average researcher—you don't need a degree in bioinformatics—it's comprehensive, looking at the totality of the information currently available, and it has monitoring agents that keep users up-to-date on changes in the public and proprietary data. And the best part is it's free. DoubleTwist.com will be offered at gold, silver, and bronze levels; and while the gold and silver levels will have a price tag, many elements of DoubleTwist.com will be freely available at the bronze level to all researchers.

How Does DoubleTwist.com Work? (Back to Top)
Using DoubleTwist.com involves a couple of easy steps:

• Log onto the secure web site.
  
• Enter your sequence or sequences as a query (and while complete information on pricing is not yet available, something like ten sequences can be entered for free).
  
• Select and configure agents—the research agents will answer whatever questions you choose (structure, similarity, function, patents), profile agents will tell you everything that is known about your sequence, and monitor agents will update you daily or weekly as new information becomes available.
  
• Do nothing, while the agents take over and apply the appropriate algorithms over multiple databases (among them SwissProt, TREMBL, dbEST, PDB, PIR, BLOCKS+, PRODOM, PRINTS, PFAM, UNIGENE, CGAP, Patent Database, Repbase, GenBank non-redundant nucleotide database, GenBank non-redundant protein database, GenBank daily DNA database updates, GenBank daily protein database updates, Human Gene Index database, Mouse Gene Index database , Arabidopsis Gene Index database, Complete Genome Database, Comprehensive Vector Database, AlphaGene clone database, ClonTech clones & reagents , Pronet (Myriad Genetics), Microbial metabolic database).
  
• View the report—the agent will notify you by e-mail when it is completed.

DoubleTwist will accept a variety of queries types—genomic DNAs, EST's, and proteins. And to give you a flavor of the kinds of questions you can ask, here's a couple of examples of the automated agents that DoubleTwist.com employs:

• Research Agent performs an extensive series of analyses, and returns information about other identical or related sequences, including EST and genomic sequences, as well as protein structures related to the input sequence. This agent is intended to answer the request "show me everything that is known about this sequence." Answers to your questions are then summarized, with additional detail available for the drilling down.

• Cluster Retrieval Agent searches DoubleTwist's comprehensive database of clustered human ESTs for matching gene sequences. The top matching cluster is returned to you, complete with all sequence information associated with that cluster: mRNA, ESTs, and all consensi.

And There's More (Back to Top)
DoubleTwist has added some nice features to its own databases that provides information on alternative splicing sites and sequence polymorphisms, corrects errors caused by chimerisms and other cloning and sequencing artifacts, corrects insertions and deletions that result in long open reading frames, and distinguishes alternative splicing from sequencing artifacts and SNPs from sequencing artifacts.

In addition, the DoubleTwist web site will be providing various related items for genomics researchers—information on products, the latest industry news, and a user network connecting researchers for chatting or for moderated discussion groups.

View from the Lab Bench (Back to Top)
Renee Stokowski, post-doctoral fellow in Stanford's Genetics Department and beta-tester of DoubleTwist.com, finds working with the DoubleTwist.com portal a huge time saver. Before DoubleTwist, she would spend hours at a time entering data and conducting searches of the various publicly available databases. With DoubleTwist, it's all done automatically once you've entered your sequence, which is done rather easily by cutting and pasting. In addition, Renee pointed out that DoubleTwist provides academic researchers unprecedented access to proprietary databases, and though not free, it's none-the-less a definitely a boon to researchers, worth paying for.

Ready To Go (Back to Top)
A trial version of DoubleTwist.com has been launched with 10 research agents that can be applied to 10 sequences over the course of a year for free. Since not all the agents will be free forever, it's a good time to give DoubleTwist a whirl.

For more information: Nicole Litchfield, DoubleTwist Inc., 1999 Harrison St., Suite 1100, Oakland, CA 94612. Tel: 510-628-0100. Fax: 510-628-0108.

By Laura DeFrancesco