Mainly 1990). Both the programs have positive and

Mainly
there are two programs for analysis of DNA sequences,

•    Barcode of Life Data
Systems (BOLD)

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It
is a free program, which compares the DNA sequences of samples that were
identified by a taxonomist and include additional data about the sample. It was
first developed to establish high volume DNA barcode facilities and a hub for
DNA barcode information and analysis. BOLD (the Barcode of Life Database) handles
all existing barcode data extends to plant barcodes (Rathnasingham and Hebert 2007).

•    GenBank data base at National
Center for Biotechnology Information (NCBI)

 It is an on-line free genetic program (http://www.ncbi.nlm.nih.gov/genbank)
(Bensonet al., 2013) which has the
most important repositories of genetic information that compares the vouchered and
non-vouchered samples of DNA sequences and researchers submit non-vouchered.
This database is one of the most frequently used databases for genomic authentication
with a large number of data availability (Hennellet al., 2012).  The unknown
DNA sequence can be compared with known sequences accurately and efficiently by
using the BLAST tool (Altschulet al.,
1990).

 Both the programs have positive and negative
attributes and use alignment programs (Altschul et al., 1990) to determine the identity of the unknown sequence, and
also all the organisms are not available in both the databases. Researchers
need reference databases which should contain sequences retrieved from reliably
identified museum specimens to identify unknown plant material that was needed
to sample ( Mishra, 2016) and these databases were included scientific names of
organisms that have been translated by the vernacular names of the market
samples.

1.1.  Bioinformatics
tools in specific primer designing

1.       

2.       

2.1.       

2.2.       

2.3.       

2.4.       

2.5.       

2.6.       

2.7.       

2.7.1.      Basic Local Alignment Search
Tool (BLAST)

The
BLAST algorithm produced significant alignment (Altschulet al. 1997) into a score matrix and performs this database search
accurately and efficiently. Although it was not specifically designed for barcode,
it has been used continuously for barcode projects since last few years (Ford et al. 2009), and prove the accuracy of
the performance by comparing it with other methods. Comparisons based on test
datasets show that it performed better than some other methods (Little and
Stevenson, 2007). The major disadvantage of BLAST is that there are no
statistical methods, (Munch et al.
2008).

2.7.2.      Primer -Blast

The
tool Primer-Blast alleviates the difficulty in designing target-specific
primers. It offers flexible options to adjust the specificity threshold and
other primer properties.1Primer-Blast
performs a primer specificity when providing a target template and the primer
pair with specific parameters (Ye J et al.,2012).

2.7.3.      PCR test

PCR
test is a virtual PCR program that searches for perfectly matching primer
annealing sites to generate a PCR product. Linear or circular sequences can be
given as the template. If the sequences are in FASTA format then can use many
sequences at once otherwise limited to one sequence only. Products of sequences
in FASTA format are sorted by size, with a title specifying product length,
their position in the original sequence, and the names of primers that produced
them.2

2.7.4.      Multiple Sequence Alignment
(MSA) as a Bioinformatics tool for specific primer designing

By
using MSA, group speci?c primers were designed for closely related species
(Fredslund et al., 2005; Adleyet al., 2009; Yanget al., 2011).In here ClustalW was used to obtain non-homologous
alignments of sequence fragments (Thompson and Higgins, 1994; da SilveiraNeto et al., 2012) According to Eddy (1995) and
Durbin et al. (1998) small barcode
studies align two at a time while Hidden Markov Models aligns many sequences at
once. MSA might miss unique regions due to gaps within the multiple sequence
alignment process and also it is a time consuming hard task. Although ClustalW
is less accurate than some modern programs (MAFFT, MUSCLE, PROBCONS, T-COFFEE),
it is the most popular, computationally less expensive in some tasks and
performed better alignment quality (Edgar and Batzoglou, 2006).

1.2.  Automation
of bioinformatics tools by using Pywinauto and Selenium software tools

2.8.       

2.8.1.      Pywinauto

3It
is a GUI automation library, which was written by using only Python and still
developed only for Windows GUI. Simply it can send mouse and keyboard actions
to dialogs which can be controlled by both Windows and Linux, while more
complex text-based actions, browsers and Store apps are supported only in
Windows.

2.8.2.      Selenium

4As an open source Selenium is a better solution for
effective techniques in building automation for web applications. It consists
of a set of different software tools each with a different approach to
supporting test automation.5 In 2004 Huggins developed selenium for
automatically controls the browsers as there’s not available any other tool
like that. Despite all these facilities, there are some drawbacks in selenium
as it has JavaScript based automation engine and the security limitations
browsers apply to JavaScript, which creates restrictions for the power of
selenium. The WebDriver project of Stewart solved those restrictions in 2006.

2.8.3.      JavaFx

JavaFx is a software platform for creating desktop
applications with high performance. UI elements in JavaFx were defined in terms
of a hierarchical structure which is called as a scene graph and all the UI
elements (buttons, Text areas, labels) of JavaFx can be styled with CSS.5

1(http://www.ncbi.nlm.nih.gov/tools/primer-blast).

2http://www.bioinformatics.org/sms2/pcr_products.html

3pywinauto
– an open source GUI automation library.

accessed on 20/07/2017

4Selenium
HQ Browser automation < http://www.seleniumhq.org/about/> accessed on
15/07/2017

5
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