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Tools in Different Spheres of Life Sciences. J Data Mining Genomics Proteomics
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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 nucleic acids 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,
Taverna is a tool used for the construction and carrying
out a chain of activities that eases 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 analyses, 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 tool used to predict 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 rebuild evolutionary
relatedness 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 to construct guide or phylogenetic 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.