Mainlythere are two programs for analysis of DNA sequences,• Barcode of Life DataSystems (BOLD)Itis a free program, which compares the DNA sequences of samples that wereidentified by a taxonomist and include additional data about the sample. It wasfirst developed to establish high volume DNA barcode facilities and a hub forDNA barcode information and analysis. BOLD (the Barcode of Life Database) handlesall existing barcode data extends to plant barcodes (Rathnasingham and Hebert 2007).• GenBank data base at NationalCenter for Biotechnology Information (NCBI) It is an on-line free genetic program (http://www.ncbi.nlm.nih.gov/genbank)(Bensonet al.
, 2013) which has themost important repositories of genetic information that compares the vouchered andnon-vouchered samples of DNA sequences and researchers submit non-vouchered.This database is one of the most frequently used databases for genomic authenticationwith a large number of data availability (Hennellet al., 2012). The unknownDNA sequence can be compared with known sequences accurately and efficiently byusing the BLAST tool (Altschulet al.,1990). Both the programs have positive and negativeattributes and use alignment programs (Altschul et al., 1990) to determine the identity of the unknown sequence, andalso all the organisms are not available in both the databases.
Researchersneed reference databases which should contain sequences retrieved from reliablyidentified museum specimens to identify unknown plant material that was neededto sample ( Mishra, 2016) and these databases were included scientific names oforganisms that have been translated by the vernacular names of the marketsamples.1.1. Bioinformaticstools in specific primer designing1. 2. 2.
1. 2.2. 2.3. 2.4. 2.
2.7. 2.7.1. Basic Local Alignment SearchTool (BLAST)TheBLAST algorithm produced significant alignment (Altschulet al. 1997) into a score matrix and performs this database searchaccurately 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 ofthe performance by comparing it with other methods. Comparisons based on testdatasets show that it performed better than some other methods (Little andStevenson, 2007). The major disadvantage of BLAST is that there are nostatistical methods, (Munch et al.2008).2.7.2.
Primer -BlastThetool Primer-Blast alleviates the difficulty in designing target-specificprimers. It offers flexible options to adjust the specificity threshold andother primer properties.1Primer-Blastperforms a primer specificity when providing a target template and the primerpair with specific parameters (Ye J et al.,2012).2.7.3.
PCR testPCRtest is a virtual PCR program that searches for perfectly matching primerannealing sites to generate a PCR product. Linear or circular sequences can begiven as the template. If the sequences are in FASTA format then can use manysequences at once otherwise limited to one sequence only.
Products of sequencesin FASTA format are sorted by size, with a title specifying product length,their position in the original sequence, and the names of primers that producedthem.22.7.
4. Multiple Sequence Alignment(MSA) as a Bioinformatics tool for specific primer designingByusing 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-homologousalignments of sequence fragments (Thompson and Higgins, 1994; da SilveiraNeto et al., 2012) According to Eddy (1995) andDurbin et al.
(1998) small barcodestudies align two at a time while Hidden Markov Models aligns many sequences atonce. MSA might miss unique regions due to gaps within the multiple sequencealignment process and also it is a time consuming hard task. Although ClustalWis less accurate than some modern programs (MAFFT, MUSCLE, PROBCONS, T-COFFEE),it is the most popular, computationally less expensive in some tasks andperformed better alignment quality (Edgar and Batzoglou, 2006).1.2. Automationof bioinformatics tools by using Pywinauto and Selenium software tools2.8. 2.
8.1. Pywinauto3Itis a GUI automation library, which was written by using only Python and stilldeveloped only for Windows GUI. Simply it can send mouse and keyboard actionsto dialogs which can be controlled by both Windows and Linux, while morecomplex text-based actions, browsers and Store apps are supported only inWindows.
2.8.2. Selenium4As an open source Selenium is a better solution foreffective techniques in building automation for web applications. It consistsof a set of different software tools each with a different approach tosupporting test automation.
8.3. JavaFxJavaFx is a software platform for creating desktopapplications with high performance.
UI elements in JavaFx were defined in termsof a hierarchical structure which is called as a scene graph and all the UIelements (buttons, Text areas, labels) of JavaFx can be styled with CSS.51(http://www.ncbi.nlm.nih.gov/tools/primer-blast).2http://www.bioinformatics.org/sms2/pcr_products.html3pywinauto- an open source GUI automation library.