17-03-2014, 05:20 PM
Abstract—This paper highlights the features of a simple Genome
Comparison and Viewing Tool (GCVT) for comparing bacterial
genomes based on their genes, products, GC counts and genome
sizes. For selected features from the results of comparison, a
facility to perform alignment using the Needleman-Wunsch,
Smith – Waterman and ClustalW algorithms is also provided.
The software can take as input, genome files in a number of
formats namely the Embl, Genbank and Fasta formats. GCVT
also provides the facility for visualizing the relationship between
chosen features using a guide tree. A number of additional
features like the DNA to protein converter amongst many others
contribute to ease the tasks of researchers. For the convenience of
the users, the software can also take a protein file in the PDB
format and display its three-dimensional structure. Compared to
existing software like Artemis Comparison Tool (ACT), DNAVis
and inGeno, GCVT is much simpler and user-friendly.
Keywords – bioinformatics; bacterial genome; genome
comparison; genome viewing.
I. INTRODUCTION
There is a very large number of public domain databases
covering a wide range of genomic data available to researchers
in bioinformatics [1]. Genomic data are stored in several file
formats namely Embl, Genbank or Fasta, amongst many
others. Genomes of organisms can thus be compared and
viewed using the annotated information stored in these files or
the sequences.
A number of tools have been implemented to
visualize/compare genomic data based on annotations, namely
the Artemis Comparison Tool (ACT) [2], DNAVis [3] and
inGeno [4]. ACT is implemented in Java and provides an
interface for comparing a number of genome files but users
must first provide a comparison file for pairs of genome files
and this is not very intuitive to users. DNAVis is another tool
implemented in C++ and provides a real-time visualization of
DNA sequences and their comparative genome annotations.
inGeno is an interactive visualization platform for sequence
comparisons between complete genome sequences and all
associated annotations and features.
Biologists increasingly need alignment methods that can
handle long biological sequences, compare them and provide a
rich visual display of the aligned sequences and the
corresponding results. The most common types of alignment
are the pairwise sequence alignment and the multiple sequence
alignment. Some genome comparison tools provide
comparison at the sequence level, e.g. Mauve Aligner [5].
Sequence alignment helps to identify regions of similarity
between sequences [6]. Thus, the alignment of sequences is a
crucial feature for doing Genome Comparison.
A tool doing genome comparison should be able to cater
for both annotation-level and sequence-level comparison.
Thus researchers in bioinformatics require a good genome
comparison and viewing tool which will provide adequate
facilities like annotation level comparison, gene identification,
and specific feature extraction, circular and linear view of
whole genome as well as sequence level comparison in the
form of alignment. Hence, keeping all these features in mind,
an integrated package, GCVT, has been designed and
developed for the efficient viewing and comparison of
genomes.
Comparison and Viewing Tool (GCVT) for comparing bacterial
genomes based on their genes, products, GC counts and genome
sizes. For selected features from the results of comparison, a
facility to perform alignment using the Needleman-Wunsch,
Smith – Waterman and ClustalW algorithms is also provided.
The software can take as input, genome files in a number of
formats namely the Embl, Genbank and Fasta formats. GCVT
also provides the facility for visualizing the relationship between
chosen features using a guide tree. A number of additional
features like the DNA to protein converter amongst many others
contribute to ease the tasks of researchers. For the convenience of
the users, the software can also take a protein file in the PDB
format and display its three-dimensional structure. Compared to
existing software like Artemis Comparison Tool (ACT), DNAVis
and inGeno, GCVT is much simpler and user-friendly.
Keywords – bioinformatics; bacterial genome; genome
comparison; genome viewing.
I. INTRODUCTION
There is a very large number of public domain databases
covering a wide range of genomic data available to researchers
in bioinformatics [1]. Genomic data are stored in several file
formats namely Embl, Genbank or Fasta, amongst many
others. Genomes of organisms can thus be compared and
viewed using the annotated information stored in these files or
the sequences.
A number of tools have been implemented to
visualize/compare genomic data based on annotations, namely
the Artemis Comparison Tool (ACT) [2], DNAVis [3] and
inGeno [4]. ACT is implemented in Java and provides an
interface for comparing a number of genome files but users
must first provide a comparison file for pairs of genome files
and this is not very intuitive to users. DNAVis is another tool
implemented in C++ and provides a real-time visualization of
DNA sequences and their comparative genome annotations.
inGeno is an interactive visualization platform for sequence
comparisons between complete genome sequences and all
associated annotations and features.
Biologists increasingly need alignment methods that can
handle long biological sequences, compare them and provide a
rich visual display of the aligned sequences and the
corresponding results. The most common types of alignment
are the pairwise sequence alignment and the multiple sequence
alignment. Some genome comparison tools provide
comparison at the sequence level, e.g. Mauve Aligner [5].
Sequence alignment helps to identify regions of similarity
between sequences [6]. Thus, the alignment of sequences is a
crucial feature for doing Genome Comparison.
A tool doing genome comparison should be able to cater
for both annotation-level and sequence-level comparison.
Thus researchers in bioinformatics require a good genome
comparison and viewing tool which will provide adequate
facilities like annotation level comparison, gene identification,
and specific feature extraction, circular and linear view of
whole genome as well as sequence level comparison in the
form of alignment. Hence, keeping all these features in mind,
an integrated package, GCVT, has been designed and
developed for the efficient viewing and comparison of
genomes.