History
• BioEdit is a user-friendly biological sequence alignment editor and
analysis program developed by Tom Hall (Hall, 1999) in 1999 while he
was working in the department of microbiology, North Carolina State
University.
• The program is used extensively with diverse research application
ever since and quoted in many article in high ranking journals.
Contribution to research
• BioEdit is one of the most common program used in molecular
biology studies of different organisms such as Virus genomes,
Bacterial genome, plant genome and animal genome.
• Compared to BioEdit, most of sequence alignment programs do not
have many other functions or useful tools for molecular biologist. It is
due to this reason that it became very important bioinformatics tool
and more distinguished among other biological sequence alignment
programs.
Advantages
• BioEdit is user friendly and can be downloaded free of charge online
from many servers.
• BioEdit is a standalone program and has functions for many
applications
• It works under most windows version that exit today.
• BioEdit can accept a wide variety of formats that is commonly used with other bioinformatics
application. This allows the swapping of Data files between BioEdit and other programs.
• Those format includes
• rich text format *.rtf,
• fasta files *.fas *.fasta *.fst *.fsa,
• genebank files *.gbk *.gen *.gb*.gnk, *.csv, tab delimited, *.txt, excel,
• abi format chromatogram file, *.ab1 *.abi,
• sequence file, *.seq,
• Plasmid files *.pmd,
• bioedit project files *.bio,
• clustal files *.aln,
• Gcg files *.gcg,
• XML files *.xml,
• A new document can be easily initiated, data can be copied (Ctrl+C) and pasted (Ctrl+V) from
clipboard.
Disadvantage
s
• BioEdit is no longer being maintained since 2007, and the
documentation is out of date.
• The time BioEdit needs to analyze sequences increases with their
length.
• Some functions need some experience (eg. Plasmid design) and
multiple steps to perform.
• BioEdit was written for Windows 95/98/NT/2000/XP.
Requirement
• Reference sequence (that can be downloaded from the nucleic acid
sequence data bases).
• Bioedit Software that is freely available.
• Sequenced data obtained from targeted sequencing.
ALIGNMENT:
1: Copy the reference sequence from the complete gene sequence
downloaded from the nucleic acid databases.
2:Go to BioEdit and click on the file icon in the top left corner.
3: select important from clipboard.
4: Accessory application.
5:. ClustalClustal W: Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.
It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best
match for the selected sequences, and lines them up so that the identities, similarities and differences can be
seen.
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