A functional marker (indelG) developed on the LTR insertion cosegregated with the trait in the CxA F 2 progeny and was validated on a broad panel of genotypes, including all known putative donors of the nectarine trait. Analysis of genomic re-sequencing data from five peach/nectarine accessions pointed to the insertion of a LTR retroelement in exon 3 of the PpeMYB25 gene as the cause of the recessive glabrous phenotype. Careful inspection of the genes annotated in the corresponding genomic sequence (Peach v1.0), coupled with variant discovery, led to the identification of MYB gene PpeMYB25 as a candidate for trichome formation on fruit skin. Here, the position of the G locus was delimited within a 1.1 cM interval (635 kb) based on linkage analysis of an F 2 progeny from the cross ‘Contender’ (C, peach) x ‘Ambra’ (A, nectarine). The peach/nectarine ( G/g) trait was described as monogenic and previously mapped on chromosome 5. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.Nectarines play a key role in peach industry the fuzzless skin has implications for consumer acceptance. ![]() Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Conclusion preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. It is available for downloading and will run as stand-alone software. preAssemble runs under UNIX and LINUX operating systems. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. Results The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. Two major publicly available packages – Phred and Staden are used by preAssemble to perform sequence quality processing. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. This is done by the sequencer proprietary software or publicly available programs. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). Keywords: Sanger, DNA barcode, DNA sequencing, Paired-end assemblyīackground Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Conclusions: PIPEBAR and OverlapPER run on most operating systems and are freely available, along with supporting code and documentation, at and projects/overlapper-reads/. 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. Results: 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. ![]() Background: 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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