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BioEdit: Essential Molecular Biology Tool

BioEdit is a widely used freeware software for molecular biology, initially developed for biological sequence alignment editing. It offers various features such as hand alignment, plasmid drawing, and integration with other programs, making it a valuable tool for researchers. However, it is no longer maintained, and its documentation is outdated since 2007.

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Shamodi De Silva
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50 views2 pages

BioEdit: Essential Molecular Biology Tool

BioEdit is a widely used freeware software for molecular biology, initially developed for biological sequence alignment editing. It offers various features such as hand alignment, plasmid drawing, and integration with other programs, making it a valuable tool for researchers. However, it is no longer maintained, and its documentation is outdated since 2007.

Uploaded by

Shamodi De Silva
Copyright
© All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd

GERF Bulletin of Biosciences

June 2011, 2(1):60-61


Software Review

BioEdit: An important software for molecular biology

Author: Tom Hall, Ibis biosciences, Carlsbad, Ca


License: Freeware Copyright 1991- 2007 Tom Hall.
Reviewed By: Dr. Ahmed Mansour Alzohairy
Department of Genetics, Faculty of Agriculture, Zagazig University, Egypt.

Abstract
BioEdit is one of the most common program used in molecular biology studies. It was developed initially as a biological
sequence alignment editor written for Windows only. It contains many features for sequence alignments modes of easy
hand alignment, Split window view, user defined color, information based shading and auto integration with other programs
such as ClustalW and Blast. However, in the last few years it was developed dramatically to integrate many other features
and functions and useful molecular tools for molecular biologist such as several modes of hand alignment, plasmid drawing
and annotation, restriction mapping and much more. It became one of the widely used programs in molecular biology with
its multipurpose toolsin molecular biology. The freeware license and its efficient up to date modules beside its quick ability
to produce results make it one of the most popular programs for molecular biologist nowadays.

History Importable data formats


In 1999, Tom Hall (Hall, 1999) has published his work on BioEdit can accept a wide variety of formats that is
a user-friendly biological sequence alignment editor and commonly used with other bioinformatics application. This
analysis program while he was working in the department of allows the swapping of Data files between BioEdit and other
microbiology, North Carolina State University. The program programs. Those format includes (rich text format *.rtf, fasta
was used extensively ever since and quoted in many article files *.fas *.fasta *.fst *.fsa, genebank files *.gbk *.gen *.gb
in high ranking journals and used in many novel and diverse *.gnk, *.csv, tab delimited, *.txt, excel, abi format
research application (Antonis et al., 2003; Ron et al., 2005; chromatogram file, *.ab1 *.abi, sequence file, *.seq, plasmid
Chen et al., 2006; Aquifer Robert et al., 2003; Klaas et al., files *.pmd, bioedit project files *.bio, clustal files *.aln, gcg
2002). files *.gcg, XML files *.xml, acqus files, phylib files *.phy,
Contribution to research NBRF/PIR files *.pir, *.nbf and you can easily start a new
document and copy (Ctrl+C) paste (Ctrl+V) data from your
Many researchers in the field of Molecular biology have clipboard).
used BioEdit modules in during their original research.
BioEdit was used for molecular studies of different organisms Advantages
such as Virus genomes (Ron et al., 2005, Chen et al., 2006), - BioEdit is user friendly and can be downloaded
Bacterial genome (Aquifer Robert et al., 2003) plant genome free of charge online from many servers.
(Klaas et al., 2002) and animal genome (Hong et al., 2008). .- BioEditis is a standalone program and has
With many citations in peer reviewed journals, BioEdit mutable functions for many applications
became very important bioinformatics tool for molecular - It works under most windows version that exit
biologist. and more distinguished among other biological today.
sequence alignment programs (Table 1). Most of sequence - The interface is user friendly.
alignment programs do not have many other functions or Disadvantages
useful tools for molecular biologist comparing to BioEdit. - BioEdit is no longer being maintained, and
the documentation is out of date and no longer
*Corresponding author: alzohairy@[Link] maintained since 2007.

Copyright © 2011 Green Earth Research Foundation [Link]


Table 1: Some other online biological sequence alignment programme functions and availability.

GERF Bulletin of Biosciences, December 2011, 2(1):60-61 61

- Scoring in pair wise alignment functions does not - BioEdit was written for Windows 95/98/NT/2000/
agree with the example in the help document. XP.
- The time BioEdit needs to analyze sequences
BioEdit availability online
increases very with their length.
- Some functions need some experience (eg. Plasmid BioEdit can be downloaded from the following Servers for:
design) and multiple steps to perform. - [Link]
- [Link]
The limitation - [Link]
- The last version was updated in 2007 and BioEdit - [Link]
is no longer being maintained. - [Link]
genetics/[Link]

Table 1: Some other online biological sequence alignment programme functions and availability

Program Function Server


LALIGN Multiple, non-overlapping, [Link]
local similarity
mAlign modelling alignment; [Link]
models the information
content of the sequences
AlignMe Alignments for low identity [Link]
membrane protein
sequences based on various
similarity criteria
GGSEARCH, Global:Global (GG), [Link]
GLSEARCH Global:Local (GL) i?rm=compare&pgm=gnw
alignment with statistics
ClustalW Progressive alignment [Link]
MULTALIN Dynamic [Link]
programming/clustering

References 5. Aquifer RTA, Helen AV, Irene OB, Charles TR, Philip
EL, Richard D, Ken K, Sam M, Donald RM, Aaron P,
1. Hall TA (1999). BioEdit: a user-friendly biological David CW, Mary L and Derek RL (2003). Stimulating
sequence alignment editor and analysis program the In Situ Activity of Geobacter Species to Remove
for Windows 95/98/[Link]. Acids. Symp. Ser. Uranium from the Groundwater of a Uranium-
41:95-98. Contaminated. Appl. Environ. Microbiol. 69(10):
2. Antonis R, Barry L, Williams1, Nicole King1 and 5884–5891.
Sean B Carroll (2003). Genome-scale approaches to 6. Klaas V, Jeroen RB, Lieven De V, Pierre R, Stephane
resolving incongruence in molecular phylogenies. R and Dirk I,a (2002) Genome-Wide Analysis of Core
Nature. 425:798-804. Cell Cycle Genes in Arabidopsis. The Plant Cell.
3. Ron AM Fouchier, Vincent M, Anders W, Theo M 14:903-916.
Bestebroer, Sander H, Derek S, Guus F Rimmelzwaan, 7. Hong XW, Zhang YP, Chu YW, Gao HF, Jiang ZG,
Björn O and Albert DME Osterhaus (2005) Xiong SD.(2008) Complete sequence determination
Characterization of a Novel Influenza A Virus and phylogenetic analysis of FKN among seven
Hemagglutinin Subtype (H16) Obtained from Black- higher primates including homonids and Old World
Headed Gulls. J. Virol. 79(5): 2814–2822. Monkeys. Yi Chuan. 30(5):595-601.
4. Chen H, Smith GJD, Li KS, Wang J, Fan XH, Rayner
JM et al. (2006) Establishment of multiple
sublineages of H5N1 influenza virus in Asia:
Implications for pandemic control. Proc. Natl.
Acad. Sci. USA. 103(8):2845-50.

[Link]

Common questions

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One major limitation of BioEdit is that it has not been updated or maintained since 2007. This means that documentation may be outdated, and any bugs or compatibility issues with newer operating systems are unlikely to be resolved .

BioEdit was initially developed by Tom Hall in 1999 as a user-friendly sequence alignment editor for Windows. Over the years, it has dramatically expanded its features to include diverse molecular biology tools, making it an essential program for researchers. Its extensive use in significant genome studies across organisms has established BioEdit as a pivotal tool in the molecular biology community, evidenced by numerous citations in peer-reviewed journals .

BioEdit offers several advantages for user experience, including a user-friendly interface and the ability to be downloaded for free from the internet. Its standalone nature and adaptability with most versions of Windows enhance its accessibility. Additionally, it provides multiple functional applications within a single program, making it convenient for users to conduct various tasks without needing additional software .

BioEdit has significantly contributed to molecular biology by facilitating various studies involving viral, bacterial, plant, and animal genomes. Its modules have supported research in characterizing virus genomes and exploring complex molecular phylogenies. BioEdit has been cited in numerous high-ranking journals and has been pivotal in studies examining novel virus subtypes, bacterial genome analyses, and plant genome investigations .

BioEdit facilitates integration with other bioinformatics tools like ClustalW and Blast through features like auto integration and support for various file formats such as fasta and genebank. This capability allows researchers to easily expand their analysis by combining BioEdit's functionalities with other specialized tools, enhancing the depth and scope of their research endeavours .

BioEdit's compatibility with a wide range of file formats, such as fasta, genebank, tab-delimited, and XML, enhances its utility by allowing seamless data interchange between BioEdit and other bioinformatics software. This compatibility ensures that users can integrate data from various sources and formats into BioEdit for analysis, thus enhancing its function as a versatile tool for molecular biological research .

Users might encounter challenges with BioEdit in plasmid design and sequence analysis due to the complexity and number of steps required. While the software supports these functions, it necessitates some level of experience to execute these tasks effectively. Additionally, the time required for analyzing sequences increases substantially with the sequence length, which may be cumbersome for large datasets .

BioEdit distinguishes itself from other sequence alignment programs through its integration of various molecular biology tools, which include modes of easy hand alignment, split window view, user-defined color settings, and information-based shading. Additionally, it offers auto-integration with programs like ClustalW and Blast. Moreover, BioEdit provides functionalities for plasmid drawing, annotation, and restriction mapping, and supports a wide variety of file formats. These features, combined with its free availability, make it a standout option among similar software .

The free availability of BioEdit has significantly contributed to its popularity among molecular biologists by lowering the barrier to access and allowing widespread use in academic and research settings without additional costs. This has enabled many researchers to adopt it for various studies, further solidifying its role as an essential tool in the field of molecular biology .

The lack of recent maintenance on BioEdit implies potential future challenges, such as incompatibility with newer operating systems and inability to address software bugs, which might limit its long-term viability and effectiveness for researchers. As technology evolves, such stagnancy could drive users towards alternative, more frequently updated software solutions .

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