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Reviewed by
(Posted September 5, 1997 ? Issue 15; archived September 19, 1997)
Test Platform:
Power Macintosh 7200/90 running System 7.6 (32 Mb RAM)
Modern biological research often requires sifting through and analyzing mountains of DNA sequence data. Such tasks have rendered the computer as essential a tool to the molecular biologist as restriction enzymes. Lasergene, developed by DNASTAR, is a powerful DNA analysis package designed to tackle the largest projects involving thousands of contiguous sequences. Despite its power, it remains easily accessible for performing basic DNA analysis such as restriction maps and sequence alignment. Lasergene is one of the few software packages able to support a sequencing project at every level from initial data entry to final sequence analysis.
Lasergene is not a single program but rather a suite of several
stand-alone applications, each designed for separate tasks. The full software package is
composed of seven separate modules that can be purchased together or
individually, depending upon the user's needs. All Lasergene modules are
controlled by a small central application called Lasergene Navigator, which
upon being launched provides a menu leading to each of the specialized
applications (see figure 1). This modular design has both advantages and
disadvantages. The individual modules have small RAM requirements, so memory
is not wasted in running a single huge application. The modular nature of
Lasergene also provides the flexibility of choosing the individual software
components most relevant to specific research needs, and enables
DNASTAR to provide the most up-to-date modules without having to
upgrade the entire suite. On the other hand, having to launch separate
applications to edit a DNA sequence and generate a restriction map can be
annoying.
DNA Sequence Editing and Analysis
The Lasergene module EDITSEQ is a simple tool for entering and editing DNA sequence data. EDITSEQ was able to import sequence data flawlessly from a variety of applications and database formats. Once data has been entered, a digitized voice can be used to read back the sequence for easy proofreading. This module is also used for basic sequence analysis such as searching for open reading frames and translation into the corresponding protein sequence. A library of genetic codes is provided for translating DNA sequences; it can also be configured by the user.
Sequencing Project Management
The SEQMAN II module of Lasergene provides all the tools necessary to
control huge sequencing projects. Chromatogram files generated by automated
sequencers such as Applied
Biosystems' 373 or Pharmacia's
ALF can be directly imported into SEQMAN (see figure 2). SEQMAN files are stored in
the form of projects into which individual sequences can be added or
Figure 2
deleted. Up to 8,000 individual sequences can be compiled into a single
project, assembled into a contig and then exported as a single sequence
file. One very impressive feature of SEQMAN is its ability to automatically
recognize and remove contaminating cloning vector sequences from the ends of
inserts. The software comes with a large library of common vector sequences
that can be edited by the user. Once a contig has been assembled, the final
product can be displayed as a sequence alignment or a strategy view (see
figure 3).
Figure 3
Restriction Analysis and Mapping
Undoubtedly the most commonly used DNA sequence analysis is the restriction
enzyme map. Lasergene includes a highly professional restriction map
generator called MAPDRAW. Restriction maps can be created in standard table
Figure 4
formats or in any one of several graphical representations (see figures 4
and 5). In addition to restriction sites, other DNA features such as
promoters and introns can be displayed on the maps. All features of the
restriction maps can be configured by the user. Graphical maps made by
MAPDRAW are not only useful for reference purposes but are of sufficient
quality for presentations or publication.
Figure 5
Multiple Sequence Alignment
The Lasergene application MEGALIGN can perform alignments of multiple
DNA sequences, protein sequences, or combinations of both. Sequences are
aligned using algorithms from either the Jotun Hein or Clustal methods, and
all alignment parameters are configurable by the user. The final output of
sequence alignment can be displayed as either an alignment report or a
phylogenetic tree (see figure 6) and are of publication quality.
Figure 6
PCR Primer Selection
The PRIMERSELECT module of Lasergene is an invaluable tool to anyone performing PCR. After providing a set of starting conditions and a template sequence to be amplified, PRIMERSELECT provides a list of potential primer candidates. The suitability of primer pairs can be ranked on the basis of user-defined criteria such as minimizing chances of primer secondary structures and false priming sites.
Protein Analysis
In addition to DNA sequence analysis, the Lasergene application PROTEAN
can perform an array of analysis on a given protein sequence. PROTEAN
calculates theoretical properties such as hydrophobicity, hydrophilicity,
surface probability and antigenicity, and presents the data in a series of
plots called an assay document (see figure 7). Simple structural
features such as alpha-helixes, beta regions, turn regions, and flexible
regions can also be predicted. PROTEAN can also search for known protease
digestion sites within the primary protein sequence. Although interesting
and pleasing to the eye, the information provided by PROTEAN is less
practical than educational.
Figure 7
Biological Database
Lasergene also includes several biological databases, provided on four CDs. The complete nucleotide listings from GenBank and EMBL are provided, as well as the protein sequence databases of NBRF-PIR, SWISS-PROT, Translated GenBank, and PROSITE. A database of crystallographic protein structures is also included. Updated versions of the databases are provided every two weeks by DNASTAR. The databases are accessed using a rapid and intuitive search engine called GENEMAN. GENEMAN can also display the 3-D crystallographic structures in the database.
The sheer vastness of the software results in a steep learning curve for the new user but is worth the effort. Having to move around within the seven different applications that make up Lasergene can be daunting at times. If you get lost, Lasergene provides extensive online help that can be accessed through the apple guide menu. One unfortunate omission in the Lasergene package is direct database access over the Internet from within the program suite. The ability to import sequence data from Internet sources such as NCBI directly into DNA analysis software is a very useful feature that is currently lacking in Lasergene. Of course one can still copy and paste sequence information obtained by searching the database with a Web browser, but direct access from within Lasergene is a useful feature worth implementing.
DNASTAR has gone to great lengths to create a polished DNA analysis package that anticipates the computing needs of molecular biologists. The full Lasergene package is a complete software solution for laboratories performing large sequencing projects requiring a diverse array of sequence compilation and analysis.
Lasergene is available for Macintosh and Windows. The Windows version of Lasergene requires a 386 or higher processor and runs on Windows 3.1, Windows 95, or Windows NT. The Macintosh version will run on any 68000 or Power Macintosh processor and is Power PC native. Both platform versions require about 30 Mb of free hard disk space and 8 Mb of RAM.
The complete Lasergene package is available from DNASTAR, Inc. The various Lasergene modules can be purchased individually except for EDITSEQ, which is included free with the purchase of any of individual module. Contact DNASTAR for current pricing information by e-mail at sales@dnastar.com or support@dnastar.com, by phone at (608) 258-7420, or by fax at (608) 258-7439. A demonstration version of Lasergene can be downloaded from the DNASTAR Web page.
Jose G. Teodoro, Ph.D., is a postdoctoral fellow at the Howard Hughes Reseach Laboratories in Worcester, Massachusetts.
