B RIEFINGS IN BIOINF ORMATICS . VOL 8. NO 6. 457^ 465 doi:10.

1093/bib/bbm039
Advance Access publication August 22, 2007

BioManager: the use of a bioinformatics

web application as a teaching tool
in undergraduate bioinformatics
training
Sonia Cattley and Jonathan W. Arthur
Submitted: 6th June 2007; Received (in revised form) : 22nd July 2007

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Abstract
The completion of the human genome project, and other genome sequencing projects, has spearheaded the
emergence of the field of bioinformatics. Using computer programs to analyse DNA and protein information has
become an important area of life science research and development. While it is not necessary for most life science
researchers to develop specialist bioinformatic skills (including software development), basic skills in the application
of common bioinformatics software and the effective interpretation of results are increasingly required by all
life science researchers. Training in bioinformatics is increasingly occurring within the university system as part of
existing undergraduate science and specialist degrees. One difficulty in bioinformatics education is the sheer number
of software programs required in order to provide a thorough grounding in the subject to the student. Teaching
requires either a well-maintained internal server with all the required software, properly interfacing with student
terminals, and with sufficient capacity to handle multiple simultaneous requests, or it requires the individual installa-
tion and maintenance of every piece of software on each computer. In both cases, there are difficult issues regarding
site maintenance and accessibility. In this article, we discuss the use of BioManager, a web-based bioinformatics
application integrating a variety of common bioinformatics tools, for teaching, including its role as the main bioinfor-
matics training tool in some Australian and international universities. We discuss some of the issues with using
a bioinformatics resource primarily created for research in an undergraduate teaching environment.
Keywords: biomanager; undergraduate; bioinformatics; interface; integrated; teaching

INTRODUCTION with a truly cross-disciplinary set of skills who are

Over the last decade, bioinformatics has rapidly able to create or modify bioinformatic software
advanced in importance as a field of study. A large applications to address questions in life science
number of specialist undergraduate and postgraduate research programs. The alternate stream aims to
degrees have appeared in universities and colleges provide life science researchers with an applied
across the globe demonstrating a perceived need for knowledge of how to work existing programs,
bioinformatics knowledge and training both now apply them to specific situations and competently
and in the immediate future [1, 2]. These courses fall interpret the results [3]. These students generally do
in one of two streams. There are degrees structured not have a background in computer science and
to include intensive training in both biology and are usually not familiar with the Unix or Linux
computer sciences, in order to produce individuals operating system under which many bioinformatics

Corresponding author. Sonia Cattley, Sydney Bioinformatics, Medical Foundation Building (K25), The University of Sydney, Sydney
NSW 2006, Australia. Tel: þ61 2 9036 3306; Fax: þ61 2 9036 3234; E-mail: [email protected]
Sonia Cattley is the Education Officer at Sydney Bioinformatics and is charged with training scientists in workshops around Australia
with the application of bioinformatic tools in relation to their particular area of study.
Jonathan Arthur is the Director of Sydney Bioinformatics. He is also a Senior Lecturer in Bioinformatics within the Faculty of
Medicine at the University of Sydney.

ß The Author 2007. Published by Oxford University Press. For Permissions, please email: [email protected]
458 Cattley and Arthur

applications are run. Furthermore, many of these examples by combining two or more applications
students are interested in making effective and in the solution of a particular problem, as output
appropriate use of bioinformatics applications for from one application needs to be cut and pasted to
furthering their biological research, rather than be used as input for another, often with reformatting
seeking to understand the information technology of the data required in between the cut and the paste.
and algorithms in, and of, themselves. This The educator must also constantly revise the training
latter stream is generally included as part of a material to reflect changes in the Uniform Resource
biotechnology or general biological science degree. Locator (URL) of the resource. Finally, many online
BioManager has been utilized as a training environ- resources are not hosted on dedicated servers and
ment within this latter stream in Australia, New thus may periodically become unavailable or may
Zealand and Malaysia. not return results in a reasonable space of time due to
Students graduating in molecular biology, veter- fluctuating load. In a study of the stability and

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inary science, agricultural science and medical persistence of URLs published in MEDLINE, Wren
science, are expected to have a rudimentary knowl- [7] found only about 63% of URLs were consistently
edge in the application of some basic bioinformatic available with another 19% available intermittently.
programs. At the most rudimentary level, this would Sometimes, the conduct of the class itself, where
include familiarity with several common, online data multiple students are submitting similar analyses at
repositories, such as UniProt [4] and GenBank [5], as roughly the same time, can trigger a collapse in the
well as the use of BLAST [6] (Basic Local Alignment server or a significant delay in response time.
Sequence Tool) for identifying sequence similarities An alternative solution is to download and install
in both DNA and protein sequences. More usefully, the various bioinformatics applications on a local,
the researcher should also receive training in mul- central server at the institution conducting the
tiple sequence alignment, polymerase chain reaction teaching or independently install the software on
(PCR) primer design, restriction mapping, evolu- multiple computers within the class room. Once
tionary phylogeny, gene detection, microarray installed, access to the central server is generally
analysis, protein structure and function prediction, configured to be available only through a series of
proteomic protein identification and characteriza- computers or terminals used by the students and
tion, motif searching and sequence assembly. networked with the central server or through a
Depending on their area of research their may be specific portal created for the purpose of offering the
additional areas, where training is required or more training. Thus, student access is limited to class time
depth is required in certain of the above areas. While and this may hamper the ability of some students to
the theory behind these techniques can be ade- complete extra work, such as assignments, using the
quately covered through standard lecture commu- programs [8]. Individual installations on every
nication, the practical applications require a degree machine are also problematic. While technology to
of ‘hands-on’ computer interaction, in order to create and propagate machine images can ameliorate
sufficiently learn the concepts. the need for a repeated, laborious installation on
There are a number of different ways a course can every machine, such technology often still requires
be structured around these multiple applications. input from a specialist in systems administration to
Many, although not all, of the software applications manage the process. Furthermore, students still have
are made available as web applications by the insti- limited access to the applications for homework and
tute or group providing the application. Students can assignments outside of class time. In small depart-
access each application as needed through the ments, or where the bioinformatics component
corresponding web site. This method has several consists of only a minor component of the subject,
difficulties. In most instances, each application is the time and cost involved in setting up and
hosted on an individual site. In order to cover all the maintaining such a system is difficult to justify.
applications, students must visit each different site Sydney Bioinformatics and one of its predeces-
in turn. Some students find this makes it difficult sors, the Australian Genomic Information Centre
to maintain concentration, as they are constantly (AGIC), through the Australian National Genomic
moving between web sites, and many more find it Information Service (ANGIS, www.angis.org.au) has
frustrating and inconvenient. It is also difficult for provided a UNIX (1991–present) and web-based
educators to construct meaningful biological (1996–present) bioinformatics interface for academic,
 BioManager: a teaching tool 459

government, non-profit and industry researchers subject to fluctuations due to the use of other non-
since 1991. Whilst its main purpose is to provide related applications on the same server. Finally, the
for the needs of Australian researchers, it is available integrated nature of the BioManager environment
throughout the world and already used in New provides the student with the same ‘look and feel’
Zealand and Malaysia. The current web interface, to the different applications, aiding in concentration
BioManager, was installed in 2001 and has over 2800 and reducing frustration and inconvenience, and
active research-based users. This system is a web enables examples involving multiple applications to
application and is thus potentially accessible any- be constructed by automatically moving output from
where in the world via the Internet. The application one application into a second application via the
currently runs on a group of servers including a Sun correct data transformations.
E450 (2
440 MHz CPUs, 2 GB RAM), a Sun
E3500 (6
400 MHz CPUs, 2 GB RAM, 2 TB HD)

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and six Sun Blade 100s (each 480 MHz CPU, 1 GB UNDERGRADUATE APPLICATIONS
RAM) although, at the time of writing a major At present there are 28 courses across 17 universities
upgrade of the hardware to two Sun V890 (8
dual around the world using the BioManager interface as
core 1.2 GHz CPUs with 32 GB RAM) backed by a part of their bioinformatics undergraduate training
4 TB high performance storage area network was (Table 1).
underway. BioManager integrates over 280 bio- The BioManager interface allows teachers to
informatic programs and sequence databases (a list create tutorials using a series of standard bioinfor-
can be found at http://www.usyd.edu.au/sydney matic programs incorporated into a web interface.
bioinformatics/pdfs_docs/bioman_programs_and_ Thus, no specialist software is required to be installed
dbs.pdf) from a range of different software packages, on the student computers: only a Java-enabled
making it more comprehensive than graphical user internet browser under a Windows, Apple or
interfaces to single packages such as EMBOSS Linux/Unix operating system. The current version
explorer and wEMBOSS, which integrate the is known to work on Internet Explorer v6 and v7 as
applications from the popular EMBOSS package. well as Firefox, together comprising about 91%
The installed packages are periodically updated as of browser usage (http://www.w3schools.com/
new versions become available, in order keep the browsers/browsers_stats.asp). Furthermore, its wide
analyses completed through BioManager up to date.
Table 1: The table shows a list of Australian and
Furthermore, the system is built in a modular fashion
international universities using BioManager as an under-
to allow BioManager staff to continue to expand graduate training tool in 2006/2007 and the approximate
the list of packages available through BioManager number of students from each university.
as required. In addition, the provision of a storage
facility to contain user sequence and results files University Number of
allows BioManager to provide a seamless workstation students
for bioinformatics analyses. Charles Darwin University 12
While the main focus of BioManager has been in Flinders University 104*
providing a service for researchers, academics using Monash University 414*
Monash University, Malaysia 83
the system have begun to use the interfaces in their Otago University, New Zealand 52*
undergraduate classes. This has happened gradually, Royal Melbourne Institute of Technology 26*
starting with the UNIX interfaces, and progressing University of Adelaide 60
University of Melbourne 78*
through other interfaces as they have been made University of New England 26*
available. Using BioManager precludes the need for University of South Australia 26*
program installation or maintenance by the educator University of Sydney 260*
University of Technology, Sydney 26*
or the student. The online interface allows the University of Wollongong 50
students to access the interface from their home University of Western Sydney 26*
computer, facilitating further study or the comple- University of Western Australia 52*
University of Queensland 20
tion of assignments outside the class room. The Victorian University of Technology 26*
BioManager servers are dedicated to this purpose
ensuring the URL of the software is constant and *Estimated on the basis of the number of BioManager logins assigned
load on the server is properly managed and not for the class.
460 Cattley and Arthur

Share and Import Files List of all programs

Show all programs

Select accession number and database

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Type of file
x

Select a file

Figure 1: A screenshot of the BioManager workbench. Selecting the GO option will extract all suitable programs
to analyse the selected file.

use as a research tool, means it is used in numerous to their account at a later time to view the results
environments, including remote areas of regional (Figure 1). As the computationally intensive analyses
Australia with less reliable internet connection and are run via a queuing mechanism the user interface is
reduced access to bandwidth, and sites outside of relatively ‘light’ and can be accessed worldwide over
Australia. There have been few, if any, reported a regular internet connection.
difficulties arising from the specific environment One of the main features of BioManager is the
where BioManager has been used. automatic formatting of an output file from one
The interface, and all generated data, is centrally program in such a way that it can be used as the input
housed on a server at the University of Sydney. for a related program even where the two programs
Access is via the web using a login and password are not from the same package. For instance, a
assigned by the tutor. Each student is given a unique multiple sequence alignment generated through
account and all files created during the class are ClustalW [9] can be used as input to a phylogenetic
stored in this account. The account can be accessed program from the Phylip [10] package. All format-
at any time and at any location. The tutor can share a ting requirements between suites of programs are
series of files with all students and students can share dealt with automatically by the BioManager applica-
files between each other (to facilitate working on tion. This prevents the need to download and install
group assignments). Bioinformatics analyses are run applications to handle the format changes, where
on the central server. All analyses are completed via a such applications exist, or perform the changes
queuing mechanism, being directed to the most manually, where they do not. It also allows the
appropriate available processor. Students do not need student to concentrate on the biological analysis
to wait until the job has finished but can come back without regard to data format transformation.
 BioManager: a teaching tool 461

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Figure 2: Screenshots illustrating the BioManager History View. An electronic record is kept with every analysis.
Options used for the analysis and the various data files generated and used along the way are stored and can
be viewed using the History option.

Students wishing to understand more about the data to the biological conclusions generated by their
underlying file formats can still access the raw file analysis.
formats as required. In feedback from the universities concerned, all
BioManager also allows both program directed (‘I classes have some formal class time dedicated to the
want to create a phylogenetic tree—what program interface, where students submit the same analyses at
can I use to do that and which of my data files can be roughly the same time from multiple computers as
used as input?’) and data directed (‘‘I have a sequence they work through set exercises. At other times,
I want to know more about—what program or students either work on the system in their own time
analysis can I use on this file?’’) approaches using or continue working at pre-determined class times
either the Program Index or the Workbench, but on their own projects. Here, job submissions
respectively. This helps guide the student to the are more sporadic and there is not the en-masse
required data or alternatively make the student aware submission as seen in the initial class or classes. In
of different ways of analysing their data they may not more than half of current classes, students are given
have been aware of previously. assignments based on the use of BioManager.
BioManager saves the history of all analyses The University of Sydney offers a number
completed. This history can be displayed by viewing of Units of Study that include teaching in the
an output and selecting the History view option. In field of bioinformatics. Some of these units make
addition to the ancestry of the result (sequences and use of the BioManager interface (e.g. Mole-
other output files generated along the path to the cular Biotechnology—MOBT3101, Molecular
final result), the parameters used in the generation of Genetics and Inheritance—BIOL5001, Pharmaco-
the select result are recorded (Figure 2). This allows kinetics and Pharmacogenetics—PHAR3630, Cell
students to review their work and more fully Biology 1B—VETS1018 and Genetics and
understand the process of moving from their original Biometry—VETS2009) while others do not
462 Cattley and Arthur

(e.g. Bioinformatics—INIM5006), mainly according complete, even when utilizing powerful hardware.
to the content of the unit of study. For example, This is due to the inherent, computationally intense
BioManager currently focuses on genomic, nature of the algorithms themselves. In a research
comparative genomics and sequence-based bioinfor- situation, this length of calculation is understood and
matics. Thus, teaching in other areas of bioinfor- factored into the individual research plan. In a class
matics, such as microarray analysis, currently makes situation, even an analysis taking up to 20 min may
use of other software packages. Our experience has cause difficulties in regard to teaching. Given the
shown a number of advantages for both teachers and output of these analyses are often needed as input for
students in making use of the BioManager environ- the next part of the student exercise, slow analyses
ment. These have been outlined earlier. Indeed, in at may limit the amount of material covered in the class
least one unit of study relying on bioinformatics and break student concentration on the task.
software outside the BioManager environment, The creation of a ‘course database’, a subset of

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a strong preference is given to the use of online sequences in the full GenBank and SWISS-PROT
resources. This, at least, reduces the burden of databases, to be used in place of the standard
systems administration to install and upgrade the databases in class situations, helps to make teaching
bioinformatics software and databases on all the of these lengthy analyses more timely and practical.
machines in the class room, which remains sub- This database will be significantly smaller (by a factor
stantial even after the use of imaging technology to of 100), so BLAST jobs will be completed in a more
rapidly transfer an installed environment from one timely fashion. The sequences to be placed into these
machine to another. databases will be chosen based on sequences used
Informal feedback received from academic staff in the current classes. In terms of the statistical
associated with the current 28 courses across 17 significance of resultant hits, the situation is analo-
universities, and others who have used BioManager gous to running BLAST against Swiss-Prot as
for teaching over the last 15 years (see Ai et al. [11] opposed to the entire UniProt database: the change
for an example of an approach to teaching including in database size impacts on the actual numbers but
BioManager), has largely echoed our experience of not the principles of how to assess the statistical
the benefits of using a system like BioManager for significance of results. Running BLAST using the
teaching while, of course, also providing feedback on Course DNA Database produces a result in <30 s as
the BioManager application to be used in further opposed to 30 min with a large-class, en-masse
development of the system. While beyond the scope submission. The result is obviously not an exhaustive
of this article, a formalized comparison of different search against the available sequence information but
modes of teaching delivery would be informative for is sufficient for a class demonstration and training
further planning of teaching strategies. purposes. In the event there is an assignment
requiring a more intensive search, there is still the
option of using the full GenBank database.
USING A RESEARCH TOOL AS However, as most assignments are completed in
A TEACHING AID the students own time, the longer analysis times are
As stated earlier, the BioManager application was usually not as critical.
designed for researchers and not as a teaching tool.
Hence, a number of issues specific to the teaching General introductory tutorials
situation arise when this research tool is used as a Educators are usually more interested in teaching the
teaching aid. From communications with class tutors students how to answer biological questions using
using the system, and our own experience, many of the bioinformatics resources available, rather than
these issues are relatively easily addressed to improve basic instruction in the BioManager interface
the learning experience of the students. itself. However, a lack of knowledge about the
BioManager interface and specific tutorials on
Lengthy analyses how to correctly operate individual programs
Some bioinformatics analyses, such as searching for (e.g. phylogeny, protein analysis, etc.) within the
sequence homologues using the local sequence interface can impede on the ability of students to
alignment algorithm of BLAST and some phyloge- grasp the computational biology being demonstrated
netics analyses, take a reasonably long time to in the course. While class requirements are different
 BioManager: a teaching tool 463

between universities, the use of the BioManager various bioinformatics applications. This is essential
interface is a common need of all courses. to ensure researchers can use the applications in the
To address this need we have created an most effective way. However, the range of options
introductory tutorial, freely available for download can, at times, be confusing to a student who is
(http://www.usyd.edu.au/sydneybioinformatics/ learning to use the application for the first time.
pdfs_docs/bioman_intro.pdf). This tutorial can be This can be addressed by preparing the classes in
used as part of the first formal class session. It is such as way as to concentrate on the main parameters
planned for additional tutorials to be added at a later and options. In addition, we are currently exploring
stage. the possibility of modifying the parameter selection
pages to reduce the number of options available
Rogue analyses when the tool is accessed by a class account to allow
Care must be taken to ensure students do not send in students to focus on the key parameters.

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untenable jobs that will use up valuable CPU with
no chance of completing successfully within the time
Communicating with student
frame of the class. These rogue analyses occur in From time to time, issues arise where the operation
a number of ways. In one situation, the student
or maintenance of the BioManager application may
may unknowingly submit inappropriate input data
impact on student’s completion of class work or
or choose inappropriate search parameters. For
assignments. For example, if a student submits an
example, multiple sequence alignments where the
inappropriate analysis that becomes a rogue analysis
resultant alignment is well over the 10 000 base pair
requiring a system administrator to stop the analysis,
limit set by the program can unproductively use
it is important the student be informed so they know
CPU time on the server. In some cases, the interface
the analysis was not completed and they do not
can check for the validity of input and reject, or at
submit the analysis again until the correct use of the
least question, inappropriate jobs. However, it is
application and limits on the analysis are understood.
common for input to be technically valid but
To address this issue, students can personalize
computationally untenable. In the example men-
their accounts by adding their name and email
tioned earlier, the individual sequences may be
address. This allows Sydney Bioinformatics staff to
within the 10 000 base pair limit but the resulting
contact them directly in the event that there is an
alignment exceeds the limit and stalls the sequence
issue regarding one of their analyses. Educators are
alignment program. Additionally, where many
encouraged to have students personalize their
parameters are required for a particular application,
accounts in this manner. In addition, a Forum has
the interface is precluded from determining all
been created for students and researchers alike
possible invalid combinations of input parameters
(http://forums.angis.org.au/) to post questions
by the combinatorics of the situation.
regarding the use of BioManager and an email
In a second situation, the student may simply not
helpdesk ([email protected]) also exists. This pro-
be aware of the approximate time scale of the
vides students with additional help in regard to the
requested analysis. This usually occurs in the context
use and operation of BioManager to augment the
of assignments or less directed exercises, where
students ‘try out’ different analyses. This can lead guidance provided by their educator.
to jobs still being processed beyond the end of the
class time, when they have ceased to be needed but Load balancing for research and teaching
continue to use valuable CPU time. One area of major concern is the potential for large
Education about appropriate limits for various classes to interfere with the use of BioManager by
programs can help address this situation in both of researchers due to the large load on the system
the above circumstances. In addition, we are able to caused by such classes. During heavy periods, when
monitor CPU usage during class sessions to capture there are more than one large class using the system,
accidental submission of inappropriate analyses. and when the class is formal (i.e. each student is
completing the same analyses at roughly the same
Excess parameters time in line with the class exercises), it is possible that
As a research tool, BioManager provides the full researchers may experience a delay while class jobs
range of options and parameter selections for the are being processed.
464 Cattley and Arthur

This can be addressed by limiting the number advantageous by time-poor students. While the use
of analyses students can simultaneously submit. of BioManager, created as a research tool, as a
Additional analyses then remain queued until the teaching aid raises a number of additional issues,
earlier analyses are complete. various strategies are relatively easily put in place to
address these. There have been some marked
Cost improvements since the above changes have been
The operation of BioManager is funded through implemented. The ability to expose students to a
the support provided by the University of Sydney, wide range of bioinformatics applications, through
occasional research grants and small, annual sub- the one consistent interface, without either the
scription fees charged to users. The service is not student or educator having to manage the installation
operated for profit. and maintenance of all these programs makes
In order to facilitate the use of BioManager BioManager a convenient resource for undergradu-

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as a teaching tool, training accounts are provided at a ate teaching and other training programs in bioinfor-
significantly reduced cost. A department is entitled to matics. Furthermore, the automatic translation of the
a number of free training accounts equivalent to the output from one application into the format for
number of research accounts it operates. The costs input into another application allows educators to
are small in comparison with typical teaching focus students on more complex and meaningful
budgets, especially if the true cost of alternatives exercises in computational biology requiring the
such as paying computer support staff to install and sequential use of several different applications.
maintain numerous software applications on multiple
machines is taken into account.
Key Points
Clearly, students trained in bioinformatics
 The ability to use bioinformatics resources effectively in life
through the use of BioManager, will need to
science research requires training on a broad range of different
purchase a subscription should they wish to continue software applications.
to use BioManager in their subsequent employment  Installation and maintenance of the many different software
(if the department they are subsequently employed applications is difficult, time-consuming and often expensive.
Using online interfaces not supported by dedicated servers,
in does not already have a subscription). Again, the is unreliable and confusing to the student due to the vast range
cost of subscription is relatively small compared to of different user interfaces and access points.
common research lab budgets, particularly if the  BioManager provides a consistent user interface to a wide range
of bioinformatics applications. Installation and maintenance of
subscription is shared with other labs in the same software is not required by either the educator or the student
department. In situations where the subscriptions and the application is reliable due to the dedicated server
cannot be afforded, students can in many cases fall required for its use as a research tool. Automated translation of
output from one software application into the required format
back on the online versions of many applications. for a second application allows the development of classes
When being trained on BioManager with its focused on the use of bioinformatics to solve real biological
common, consistent interface, the student is able to problems.
focus on the purpose of each application, the
meaning of the input parameters and the correct
interpretation of output data, rather than needing to Funding
learn the multitude of different user interfaces. Once ANGIS, including BioManager, is subsidized by the University
the application is understood, the student should find of Sydney and additionally supported by Australian and
it much easier to return to the regular web interface international researchers and teachers through subscription.
The hardware upgrade described is funded by an Australian
and understand the particular idiosyncrasies of the
Research Council LIEF grant (LE0668549).
native interface.

Acknowledgements
CONCLUSIONS The authors would like to specifically thank Dr Catherine
The BioManager interface has been well received by Abbott of Flinders University, Dr Alex Andrianopoulos of the
University of Melbourne and Dr Neville Firth of the University
the students and educators currently using it in 28
of Sydney for providing specific feedback on their experiences of
courses across 17 universities around the world. BioManager in a teaching environment. We also acknowledge
In particular, the ability to start an analysis and return other BioManager users who have provided feedback on the use
to review the results at a later time has been seen as of BioManager as both a research and teaching tool.
 BioManager: a teaching tool 465

Information about BioManager access can be found at 6. Altschul SF, Madden TL, Schaffer AA, etal. Gapped BLAST
http://www.usyd.edu.au/sydneybioinformatics/angis/biomana- and PSI-BLAST: a new generation of protein
database searching programs. Nucleic Acids Res 1997;25:
ger.shtml. Sydney Bioinformatics is a Centre of the University of
3389–402.
Sydney. A free trial period is offered for international (non-
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of URLs published in MEDLINE. Bioinformatics 2004;20:
Cattley ([email protected]).
668–72.
8. Honts J. Evolving strategies for the incorporation of
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