Therefore, Bioinformatics plays a key role in supporting and consolidating DNA barcoding efforts, from choosing the PCR primers to evaluating sequence quality and subsequent data analysis. The success of DNA barcoding for evolutionary studies depends on an accurate selection of theses molecular markers, once distinct species group show distinct speciating taxa, retention of ancestral polymorphism and hybridization. The combination of coding genes (matK, rbcL, rpoB, ycf1 and rpoC1), noncoding spacers (atpF–atpH, trnH–psbA, and psbK–psbI) and the nuclear-encoded ribosomal internal transcribed spacer (ITS2) is highly recommended to obtain an adequate species discrimination for plants. For plants, the markers of choice are the large subunit of RuBisCo (rbcL) and maturase (matK) adopted as standards, but other markers are also used. The universal barcode locus used for discriminating animal species is the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. In these cases, there are necessity of sequencing of individual specimens using genome regions in order to infer evolutionary differences and identification only. Also, DNA barcoding has been proposed for forensic identification and development of DNA reference library, since the lack of a reliable DNA barcoding reference library is the main barrier to its application Sanger technology has been widely used for aiding morphological species identification because is a useful tool for identifying genetically distinct units worthy of more intense taxonomic study and creation of reference database, such as BOLD. This approach is widely employed in biodiversity studies to identify and classify the diversity of well-known species or unexplored groups, evaluate inter- and intra-species variations, detect cryptic species or join genetically similar but morphologically distinct species. DNA barcoding is an important molecular methodology based in a short standardized polymorphic sequence capable of distinguishing species. Next generation sequencing (NGS) platforms have been used on a wide variety of omics studies for biodiversity assessment but the traditional Sanger method is still broadly used, including genetic testing and DNA barcode generation. Īdvances in DNA sequencing approaches have produced an overwhelming volume of data, followed by new data analysis software and pipelines. PIPEBAR and OverlapPER run on most operating systems and are freely available, along with supporting code and documentation, at and. OverlapPER obtained the best results compared to currently used tools when merging 1,000,000 simulated paired-end reads. OverlapPER is a novel tool for overlapping paired-end reads accurately that accepts both substitution and indel errors and returns both overlapped and non-overlapped regions between a pair of reads. It is 7 times faster than Geneious and 14 times faster than SeqTrace for processing hundreds of barcoding sequences. It is accurate as the proprietary Geneious tool and faster than most popular software for barcoding analysis. PIPEBAR is a command line tool to automatize the processing of large number of trace files. We also proposed a paired-end reads assembly tool, OverlapPER, which is used in sequence or independently of PIPEBAR. To reduce at most such interaction, we proposed PIPEBAR, a pipeline for DNA chromatograms analysis of Sanger platform sequencing, ensuring high quality consensus sequences along with efficient running time. DNA barcode sequence analysis is usually carried out with processes and tools that still demand a high interaction with the user or researcher. DNA barcodes allow a rapid species discovery and identification and have been widely used for taxonomic identification by targeting known gene regions that permit to discriminate these species. Taxonomic identification of plants and insects is a hard process that demands expert taxonomists and time, and it’s often difficult to distinguish on morphology only.
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