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sequence alignment of biological sequences using algorithms.
rebuild evolutionary relatedness among organisms.
To find motifs
in biomolecules, domains in proteins and protein binding sites in DNA.
analyze and visualize the multiple sequence alignment in biological
sequences, predict secondary structures in protein molecules.
protein sequences by multiple sequence alignment, phylogenetic analysis and
predict protein structures.
bioinformaticians who are not skillful in web services and programming by
providing interface between different tools and databases.
genome structures of human, predict exons, introns, transcriptional,
translational signals and intergenic regions, find gene or multiple genes in
It is such a tool used to find and search whole structures
present in genomic DNA of humans. GENSCAN used to predict exons, introns,
transcriptional, translational signals and intergenic regions in the DNA. Gene
or multiple genes present in DNA can also be predicted by using this tool. This
tool proved to be accurate as it predicted 75 to 80 % exons precisely. (Chris Burge, Samuel Karlin, 1997) 8.
Taverna has number of uses in constructing and performing
a sequence of activities that relaxes bioinformaticians who are not skillful in
web services and programming languages. It provides interface between
bioinformaticians and web services that helps to communicate between different
tools and databases for sequence analyses. Taverna has many services and one of
them provided by INSDC (http://www.insdc.org/ ). (Duncan Hull et.al, 2006) 7.
It is a protein sequence alignment tool used to build
alignments of protein sequences by multiple sequence alignment with great
accuracy. It is reported to be the fastest sequence alignment tool compared
with other alignment tools e.g., T-Coffee, CLUSTALW etc. It has wide range of
uses including phylogenetic analysis, to locate protein structure etc. The most
important thing of this tool is to show the evolution of sequences by graphs. (Robert C. Edgar, 2004) 6.
It a tool used to edit, analyze and visualize the
multiple sequence alignment of biological sequences and refine the sequences. It
is used to align the sequences and predict the secondary structures of the
protein molecules. It shows the alignment results by showing figures and
construct phylogenetic trees of sequences. JALVIEW 1.0 is not able to analyze
the huge and detailed tasks, so JALVIEW 2 is constructed by bioinformaticians
to perform greater tasks. (Andrew M.
Waterhouse et.al, 2009) 5.
It is a bioinformatics tool used to find out motifs in
biological sequences of biomolecules e.g., proteins and DNA. It is also used to
discover domains in proteins and protein binding sites in DNA. It can also be
used to find out repeated sequences in proteins and DNA when query sequences
are submitted into it. (Timothy L.
Bailey et.al, 2006) 4.
MEME (Multiple EM For Motif Elicitation)
is a bioinformatics tool used to reconstruct or restore evolutionary
relationships among the species or organisms. MEGA’s important feature is the
use of graphical user interface (GUI), that shows the graphical representation
of the given data, phylogenetic trees and results. (Sudhir Kumar et.al, 2012) 3.
(Molecular Evolutionary Genetics Analysis)
CLUSTAL Omega is a latest version of the
CLUSTAL programs for multiple sequence alignment of biological sequences. It
uses algorithms for construction of guide trees. The software has proved to be
better in comparison to earlier CLUSTAL series and it has great precision. The
larger alignments can be done using this tool even on home computers. (Sievers
F., Higgins D.G., 2014) 2.
Bioinformatics tools for biological
sequences are the information stored in DNA and proteins in the form of letters.
These letters are instructions and have specific arrangements given by the
nature to our DNA and from DNA to proteins. The nucleotides in DNA are
instructions that pass from generation to generation. The proteins are
macromolecules made of amino acid sequences and perform many functions of the
body. The sequences came into existence due to molecular attractions of
different molecules. Sequence analyses
is the comprehension of novel arrangement and characteristics of codes in a
biomolecule like nucleic acid and protein, that are responsible for their
operation and function. (Mehmood MA
et.al, 2014) 1. For carrying out sequence analyses, the sequences after retrieval from different
databases are refined and submitted to various tools that speculate their
features important for their function, structure and evolutionary history with
extreme precision. (Mehmood MA et.al,
2014) 1. The objective of this review is to encompass all the tools being
used for biological sequence analyses.