Overview

LifeSeq Public from Incyte Genomics is a Web-based collection of sequence-analysis tools that access an expressed sequence database from the public domain as well as a portion of Incyte's proprietary sequence database. Queries can be made against these databases either through the BLAST algorithm to match sequences, or by specific identifiers, such as Genbank ID number, keywords, or function (enzyme, function, or pathway). Retrieved sequences can be saved to a separate Workbench section in which search results, saved sequences, and purchased sequences can be organized. Sequences can also be assembled to form a consensus sequence, translated to peptide sequences, or assembled via the ClustalW method (protein-sequence alignment). While many of these tools are available separately, LifeSeq Public makes it easy to move between these tools and work with the same sequences. Furthermore, LifeSeq Public makes it easy to purchase verified proprietary sequences from Incyte Genomics. For example, users have partial access to Incyte's clone and expression array data. LifeSeq Public is appropriate for most molecular biologists doing sequence analysis. However, the real power of LifeSeq Public lies in being able to link sequence information with readily purchased sequence-specific reagents and data, such as clones and expression information.

How Long Did It Take to Learn to Use It Productively?

About ten minutes to register. About an hour to understand what each subsection could do. By the end of the day, I was comfortable with the interface and collection of tools. Keep in mind that I am familiar with several sequence-analysis programs.

Product Quality

Customizability

The only piece the user can customize is the Workbench. The Workbench forms a central repository of user-selected sequences, search results, and search histories.

Ability to Program in Scripts, Add Extension Modules, etc.

None.

Ability to Import and Export in Different File Formats

None. The only way to enter novel sequences is to paste them in FASTA format into one of the tools' input boxes. There is no way to create a new sequence entry. Sequences that are in the sequence databases are not novel and can be retrieved and saved into the Workbench. There is no export or output method.

Useful or Unusual Features

LifeSeq Public registration is free to anyone, not just research staff associated with nonprofit and academic institutions. By registering, users gain access to Incyte's enhanced cDNA database. In addition, registration includes access to LifeSeq Gene-by-Gene, a clone database enriched with proprietary Incyte sequences; the LifeExpress expression database, which uses a wide range of gene-array data; a centralized Web-based Workbench; and access to the Incyte Genomics Software Exchange, containing a collection of public-domain sequence-analysis software. Since Incyte is using LifeSeq Public to drive sales of its proprietary sequences, both purchase history and LifeSeq Public use is strictly confidential. Incyte repeatedly reminds the user of this.

Tools

Incyte's LifeSeq Public comes with a basic set of gene analysis tools:

• Search. One can search for genes in the LifeSeq Public database (see below) by a traditional BLAST search; by using a keyword or a GenBank ID number; by function (a classification hierarchy of enzyme, function, or pathway); or by unique ID number, such as a specified clone ID, GenBank identifier, LifeSeq Public Gene ID, or Incyte ID.
• Assemble, translate, align. Consensus sequences can be assembled from two or more nucleotide sequences (Phrap assembly). Nucleotide sequences can be translated into peptide sequences, and two or more protein sequences can be aligned via the ClustalW alignment algorithm. When results are listed, for example after a search, the list contains elements, such as sequences and ID numbers, that can be clicked to view the individual result or as a basis for further analysis (and, of course, purchase). These results can also be saved to the Workbench for later analysis or simply to log them. Furthermore, all these tools have a Java-based graphical viewer that allows the user to choose different views, such as to view the overall structure or to zoom to the sequence view. The graphical viewers are very good.

Database

LifeSeq Public uses a database of 1.4 million public expressed sequence tag (EST) sequences and 90,000 proprietary Incyte sequences. The sequences were obtained from human tissues and human cell lines. Incyte updates the database regularly. This database is really for those working with expressed genes.

Workbench

While not directly integrated into LifeSeq Public, the Workbench is also free to LifeSeq Public users. The Workbench is a place where users of Incyte's public-domain tools can save queries, retrieved sequences, and search history from LifeSeq Gene-by-Gene, LifeSeq Public, and LifeExpress pages. For example, if one searches for sequences that match a specific gene, results can be saved to the Workbench. Later, the user can view, purchase, or further analyze the saved data using any of the tools available.

Purchasing Sequences

While LifeSeq Public is a free, public-domain tool, the real goal is to drive the sale of proprietary Incyte sequences. In addition to offering sequences for sale through LifeSeq Public, Incyte offers other "free" search tools, such as Gene-to-Gene, which provides partial access to Incyte's subscriber database.

The ability to purchase relevant sequences without having to telephone or clone them by hand is really the strength of Incyte's online genomic tools. The fee-based version of Public is LifeSeq Gold, which provides access to Incyte's enhanced database of public and proprietary sequences.

Limitations

Navigation

In addition to LifeSeq Public, Incyte offers some other tools that can use the information accumulated in LifeSeq Public. The Workbench, mentioned above, can be used from most of Incyte's Web-based tools. While it is straightforward to add results from a tool to the Workbench, accessing the Workbench is cumbersome. Basically, there is no single menu bar that allows one-click access to the Workbench. A menu bar that unites all the different public domain tools would be useful. The current implementation requires the user to return to the top login page to enter another module.

Tools

There is no easy way to output the results of searches and alignments. Also, there are no tools for cloning, plasmid drawing, and other basic molecular-biology features. This may be in part because the analysis package is designed to drive sales, and is not a public-domain analysis tool for generating publication-quality graphics. This might not be a serious flaw, considering the intent of the tool set, which is really to help users analyze sequences and purchase new reagents to move on to the next step in research.

Comparisons with Similar Software

LifeSeq Public is the first integrated suite of sequence-analysis tools that I have used, although I have used many individual public-domain Web-based tools. Celera has a similar offering, except it seems to allow the creation of protein-sequence data sets. It is also not clear to me if the Celera database contains expressed genes (i.e., ESTs) or if it is more general (i.e., for genomic research). It would not be surprising if Celera's database contained additional information since Celera's approach is more genomics based than that of Incyte, which is largely an expressed gene company. Unlike Incyte, Celera's tools are accessible only to nonprofit, governmental, and educational users, as determined by the email address; therefore, I was not able to browse Celera's suite of tools. Other users must be approved on an individual basis. Nonetheless, Celera also uses these public genome tools as a way to advertise and sell proprietary sequence information.

Technical Support and Documentation

Online help documentation and tutorials are good. Further support is available on the Incyte support pages or via fax, email, or telephone to Incyte customer service. I asked a few questions via email but didn't receive a response after two weeks. I rate direct customer support as poor, giving technical support an overall rating of fair.

Target Users

Incyte's sequence-analysis programs are useful to any molecular biologist working with expressed genes. Molecular biologists who are in a position to buy sequence-specific, verified reagents would find these tools useful.