PRACTICAL

AIM: To study the various analysis tools of BioEdit and edit various sequences using them.

PRINCIPLE:

BioEdit is a biological sequence editor that runs in Windows 95/98/NT/2000 and is intended to provide
basic functions for protein and nucleic sequence editing, alignment, manipulation and analysis. Version
1.0 alpha was the very first version and was unfinished and very buggy. Version 1.0 alpha II was still
unfinished and had a bunch of bugs too, but several things were added and several bugs fixed. In version
2.0, an interface was added to add and configure accessory analysis applications to run via a graphical
interface created by BioEdit. Also, information-based dynamic shading of alignment positions was
added. Hydrophobicity/hydrophilicity profiles, interactive 2-D matrix data plotting and a few more
sequence manipulations were added in version 3. Version 4 added a graphical interface for drawing and
annotating plasmid vectors. In version 4.7.1 handling of sequence information and memory were altered
and a binary file format was added to allow fast saving and opening of large alignments. The sequence
capability was expanded to 20,000. In version 5, annotation of sequence automatically or manually using
all of the standard GenBank feature definitions was added. Also, at the request of Isis Pharmaceuticals,
Inc., sequence sorting and grouping, group manipulation, comment lines, and differentiation between
residue and non-residue characters was added. BioEdit is not intended to be a powerful sequence analysis
program, but is instead intended to be a user friendly interface for sequence manipulation and linking to
other, more scientific analysis programs, both local and WWW-based. It is now suitable for large
alignments (>2000 sequences). The document interface was originally modeled after the very nice
programs SeqApp and SeqPup by Don Gilbert. SeqApp (Macintosh) and SeqPup (cross-platform) are
offered free of charge from Indiana University at. An exceptional alignment program that is freely
available for Windows 95/98 is called GeneDoc. GeneDoc is very professional and has nice protein
alignment annotation and analysis, shading and structural definition features not offered in BioEdit, as
well as an internal phylogenetic tree view of alignments. GeneDoc can also be found on the World Wide
Web.

BioEdit is a C++ program written in Borland's C++ Builder. I am a graduate student in Microbiology at
North Carolina State University, and not a trained programmer. This was my introduction to the C++
language and is necessarily a side project (this is not part of my doctoral work). This program could be
much smaller and more efficient. Nevertheless, BioEdit provides an easy means for sequence alignment,
output, and some analyses.

OBSERVATIONS: These are the four haemoglobin sequences taken from NCBI. These have been
added by selecting New Alignment in the file option and then selecting Open in the File option. The
fourth sequence was added by selectiong the Import option and then the particular sequence.
The following view has been obtained by selecting the Graphical view option in the File.

The following Dot Plot has been obtained by selecting the Dot Plot(pairwise comparison) option in the
Sequence tool.
The following two printscreens consist of amino acid composition of a sequence.
The following printscreen is the Pairwise alignment.

The following is the hydrophobicity plot of a particular sequence.

The following is the printscreen is a result of selecting clustal w option.

The following is a result of BLAST from the option Accessory Application.

RESULT: The analysis was done using the various graphic and alignment tools of the software BioEdit.

CONCLUSION: