Get with the Program

It is often said that necessity is the mother of invention. In the world of bioinformatics, the need to examine and manipulate large volumes of sequence data begat specialized computer software to handle these tasks. These programs vary in terms of ease-of-use, power, and functionality. Yet they can each perform some or all of the following functions: DNA and protein sequence entry, editing, annotation, analysis, and alignment; primer identification; map making; contig assembly; "in silico" cloning; and gel prediction. Some sequence analysis programs include a broad range of these functions, whereas others include individual, task- specific modules; smaller labs with specialized needs may find that purchasing particular modules better fits their budgets. Researchers install most programs locally, on a desktop computer, but some packages are Web-accessible. Most are also Web-enabled, allowing users to download data from remote databases. Recently, companies have worked to make these programs user-friendly enough for anyone to use, often including detailed user manuals, get-started tutorials, and step-by-step protocol guides. Since our last review,1 the software market has changed somewhat. New companies on our list include ApoCom Genomics, Bioinformatics Solutions, and Paracel. DoubleTwist, supplier of TwistTools, has closed, and despite repeated efforts, we were unable to reach Gentech, Biotechnix3d's supplier, to confirm either the status of that program, or even if the company is still in business (its Web site has been under construction for some time). What follows is a round up of each company's latest offerings. CORPORATE COMPENDIUM San Diego-based Accelrys' widely known GCG® Wisconsin Package™ houses over 100 sequence analysis applications. The UNIX-based package supports Web-based access via SeqWeb®, and has a relational database version that integrates with SeqStore®, the company's Oracle-based data management and mining system. The Macintosh-compatible MacVector also offers multiple sequence analysis options and includes the AssemblyLIGN module to assemble consensus sequences. Last September, Accelrys released a Mac OS X- compatible version of MacVector. This June, the company launched its newest sequence analysis software package, Discovery Studio™ (DS) Gene. This Windows-compatible software connects to the Wisconsin Package to perform database searches with minimal data configuration, and replaces the soon-to-be discontinued OMIGA™, whose users will be offered a discounted upgrade to DS Gene. GrailEXP™, a new, advanced version of the Grail Toolkit from ApoCom Genomics of Knoxville, Tenn., predicts both protein- coding genes and functional elements. Another offering, GeneHound™, is a gene sequencing and identification program targeted for prokaryotic genomes, but which may be easily adapted to any genome. According to ApoCom's president, Robin Zimmer, the company's newest package, called Excavator (EXpression data Clustering Analysis VisualizATiOn Resource), is a gene expression database analysis application that allows the user to study functional relationships, clustering genes whose expression patterns correlate relative to time and/or altered conditions. PROSPECT, the Protein Structure Prediction and Evaluation Computer Toolkit from Bioinformatics Solutions (BSI) of Waterloo, Ontario, employs threading to predict three-dimensional protein structure by recognizing native-like folds within a sequence. The newest version, released last December, features an updated database that includes 500 new protein templates and enhanced accuracy. This past March, BSI began offering a limited version of PatternHunter--a homology software program 400 times faster than BLAST (Basic Local Alignment Search Tool) with equivalent sensitivity--to academic researchers, downloadable upon request through the company's Web site. A professional version of the program is also available, which includes several additional functions. DNASTAR of Madison, Wis., offers Lasergene, a user-friendly, modular sequence analysis software package, for both Macintosh and Windows users. Modules include: SeqManII™, a sequence assembler that supports over 10,000 sequence reads; GeneQuest™, which identifies and annotates genes; Protean™, a protein structure prediction program; MegAlign™, which aligns both DNA and protein sequences; PrimerSelect™, a primer designer; MapDraw™, a mapping program; and EditSeq™, which edits and imports sequences and annotations. The newest version includes a completely reworked, in-depth user manual, expanded Internet connectivity and import/export capabilities, enhanced displays, and new analysis features such as multiple sequence alignments using ClustalW, SNP detection, multiple consensus sequence comparison, and creation of GenBank-style features. Scheduled for release this fall, GenVision, DNASTAR's new genomic data visualization tool, will generate high-quality, publication-ready postscript images from textual data and annotations. Sunnyvale, Calif.-based Entigen's Bio-Navigator™, a high-powered suite of online sequence analysis applications, now features improved efficiency. The software can analyze multiple sequence sets simultaneously and then automatically record all steps. By selecting "History View" re-searchers can rerun analytical steps in a custom-created order on new datasets. Hamilton, New Zealand-based Genamics' Windows-compatible Expression software supports both DNA and protein sequence analyses. Features include reverse translation, degenerate DNA and protein support, distance matrices, and a plug-in architecture for software developers. Free, downloadable demonstrations and tutorials are available, as is special introductory pricing. According to Genamics codirector Marcel Dinger, an updated version of Expression is due out at the end of 2002, and will provide better support for large, genome-scale sequences. Sequencher from Gene Codes of Ann Arbor, Mich., specializes in contig assembly, but includes vector/transposon screening and heterozygote identification for mutation studies. The program can interface with several automated DNA sequencers, has a Smart Translation feature that correctly translates ambiguous, nondegenerate codons, and organizes and stores data in a compact format. Vector NTI® Suite, from InforMax of Bethesda, Md., integrates desktop analysis, data management, and visualization tools to accelerate the pace of genomic and proteomic research on both Windows- and Macintosh-based computers. According to Craig Ferri, global marketing communications director, the Suite lets molecular biologists perform numerous informatics workflows in a single, integrated, graphically rich environment that eliminates the need to reformat data. For example, scientists can use chromatogram data to generate edited and finished consensus sequences from which BLAST-generated hits can be analyzed and recovered. Vector NTI offers easy import and export of multiple data types, Internet data access, transparent data searching, annotation, illustration, publication-quality graphics, and collaborative data exchanges. The newest version adds advanced primer design, additional protein sequence annotation tools, the ability to apply standard sequence analysis tools to reference genomic sequences, and increased data throughput. San Francisco-based LabVelocity now offers subscription-based access to its Jellyfish sequence analysis package, which was previously offered free of charge. With an intuitive graphical user interface designed for everyday gene analysis, the inexpensive Jellyfish is popular both as a benchtop tool and for classroom use. As a Web-based application, users receive the latest improvements and upgrades simply by logging on. The June release lets researchers import sequences directly from public databases without additional formatting, run sequences through BLAST, and simplifies many basic sequence analysis tasks. The program runs under both Windows and Macintosh operating systems, including Mac OS X. The company offers a 30-day free trial at its Web site. Alameda, Calif.-based MiraiBio offers DNASIS Max for Windows and MacDNASIS for Macintosh users. Both offer comprehensive DNA/RNA and protein analysis features. Molecular Biology Insights of Cascade, Colo., specifically designed its Oligo program to identify potential oligonucleotide sequences for such applications as PCR, DNA sequencing, site-directed mutagenesis, hybridization protocols, and synthetic-gene construction. It uses nearest neighbor thermodynamic values to calculate and analyze an oligonucleotide's secondary structure, hybridization temperature, and biophysical properties. According to Wojciech Rychlik, a major upgrade of Oligo will be available next year that will run on UNIX-based systems (the Mac and Windows-based platforms are also still available). The new version will be fully automatable for use in real-time PCR, TaqMan® assays, molecular beacons, and multiplexing. Pasadena, Calif.-based Paracel offers several sequence data analysis tools. TranscriptAssembler™ is a high-powered software tool for expressed sequence tag-based transcript reconstruction that filters, masks, clusters, assembles transcripts, and detects alternative splice forms. Paracel's shotgun sequence assembly program, GenomeAssembler™, makes base calls from raw trace data, deletes contaminating sequences (such as vector sequences), designates constraints for sequences based on those from different subclone libraries, and assembles final contigs and scaffolds. This program is appropriate for projects ranging in size from bacterial artificial chromosomes to whole microbial and fungal genomes. Both TranscriptAssembler and GenomeAssembler automatically detect the project's data format, recognizing PHD, FASTA, GenBank, EMBL, and CAML (XML) formats. TraceTuner™ uses unique algorithms and an advanced peak-processing method for very accurate base calling, a requirement for today's high-throughput sequence analysis projects. Paracel's Filtering Package is specifically designed for sequence filtering and masking, identifying and deleting contaminating pieces of sequence that interfere with assembly steps. Finally, AGENT, Paracel's newest product, is a complete software package for sequence-based genotyping that accurately calls mixed bases and determines all mutations as compared to a reference sequence. PREMIER Biosoft International of Palo Alto, Calif., offers a variety of new sequence analysis software tools. Beacon Designer designs optimal PCR primer pairs and probes for molecular beacon and TaqMan® assays in addition to its ability to perform BLAST searches on selected sequences. Features such as melting-temperature adjustment, allele discrimination, dimer and repeat analysis, and cross-homology prevention provide for increased signal and decreased competition during multiplex real-time PCR studies. Protein Networker, a Web-based application, develops graphical protein interaction maps for all two-hybrid screen protein interactions. Array Designer is targeted for the design of hundreds of primers for DNA or oligonucleotide microarrays, and outputs the statistically best probe for each template after analysis by the National Center for Biotechnology Information's BLAST server to assure gene specificity. Primer Premier is a primer design, enzyme, and sequence motif analysis package that is also capable of supporting cross species and multiplex/nested PCR reactions. A new version of the company's vector-design software, SimVector, offers drawing tools to produce bitmapped and vector graphics. It supports in silico cloning using standard restriction enzyme methods, TA cloning protocols, Cre recombinase-based cloning, and Invitrogen's (Carlsbad, Calif.) GATEWAY™ system. Newly released in July, Premier's Xpression Primer is a PCR primer design package intended for high-throughput cloning projects for structural genomics. NetPrimer, a free primer analysis program, is also available through PREMIER's Web site. Toronto-based Redasoft offers Visual Cloning, a Web-integrated, genetic mapping and analysis software tool. Alexandra Carmichael, Redasoft's Chief Software Architect, cites three exceptional features: ease of use, superior graphics, and extensive and seamless Internet integration. The program can download sequences from online databases and create labeled graphical maps. Sequence analysis functions include an advanced search for restriction enzyme sites using REBASE's updateable database of more than 1,000 enzymes, open reading frame searches, primer design, sequence viewing and editing, and subsequence searches. According to Carmichael, Redasoft is currently developing its third-generation software package, incorporating highly advanced graphical sequence editing, virtual cloning features to accurately simulate wet lab experiments, and integration with information and related sources for increased productivity. Sci-Ed Software of Durham, NC, specializes in Windows-based personal computer programs for molecular biologists. The Clone Manager Suite includes Clone Manager, Primer Designer, and Align Plus. Each can function as a stand-alone program, but when two or more components are installed, they can integrate within the central program hub (Sci-Ed Central) and appear as one program with increased functionality. The component programs all contain a complete set of sequence editing features and database-access capabilities. Sci-Ed also offers Enhance Map Draw, an enhanced mapping program, as a separate option. Textco of West Lebanon, NH, recently released an updated version of its Gene Construction Kit™. Specializing in the graphic design and manipulation of DNA sequences as well as plasmid map drawing, the new version includes a Deluxe Importer Module for integrated GenBank and EMBL searching and Internet file retrieval/import. The new version runs natively in Mac OS X but is compatible with both Windows and Macintosh platforms; files created on either platform can be read by the opposite platform, allowing for easy data exchange between collaborators. Gene Inspector™ is both an all-inclusive sequence analysis program and a sophisticated electronic laboratory notebook. The software performs all analyses in the background, allowing researchers to continue working in the notebook section as the program tackles sequence problems. Users can design and save a suite of analyses to be run with each newly acquired set of sequence data, and the output data display format can be customized according to individual preference. Thus, analyses are automatable, and similarly formatted presentations can be generated among laboratory personnel. FREE SEQUENCE ANALYSIS For those laboratories on a tight budget, or for those who dabble only occasionally in sequence analysis, some free options are available. Though generally neither as polished, nor as integrated as commercial packages, these options can perform a surprisingly rich set of functions. Wheaton College, Mass., for instance, offers the DNA Motif Lexicon, styled after the Oxford English Dictionary, as well as other annotation tools at its Web site (genomics.wheatoncollege.edu). Wheaton's suite of free applications is a collaborative project between faculty and students in the Departments of Biology and Computer Science, and undergraduates write all the software. According to Betsey Dexter Dyer, professor of biology, the Motif Lexicon is designed to thoroughly catalogue and annotate DNA sequences of all lengths (especially intergenic) for better understanding of their roles in gene regulation. The San Diego Supercomputer Center's Biology WorkBench (workbench.sdsc.edu) allows investigators to search many public databases of protein and nucleic acid sequences. It is also integrated with several analysis and modeling tools that accept popular database sequence formats without the need to reconfigure. The free Sequence Manipulation Suite (www.bioinformatics.org/sms) is a collection of programs for formatting and analyzing protein and DNA sequences that outputs a set of HTML commands. Protein re-searchers should visit the Expert Protein Analysis System molecular biology server (www.expasy.ch), which offers a wide range of proteomics tools. For a large database of Web-based molecular biology tools, see the CMS Molecular Biology Resource (restools.sdsc.edu). Barbara A. Cunningham (barbaracunningham@hotmail.com) is a freelance writer in York, Maine. 1. J.M. Perkel, "Desktop sequence analysis software," The Scientist, 15[23]:29, Nov. 27, 2001.

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