Graph Pad Prism 7.0 (Graph Pad Software, La Jolla, CA, USA) was used for graphical representations and statistical analysis. Linear regression of standard curves of micro-Bradford assays were calculated with Microsoft Excel 2013 (Microsoft, Albuquerque, NM, USA). Spot matching of 2D-gels and 2D-immunoblots was done using Delta2D v4.6 (Decodon GmbH, Greifswald, Germany). Sequencing results were analyzed with DNA Baser v4.36 (Heracle BioSoft, Arges, Romania) and alignment was performed using BLASTn v2.8 [35 (link)].
Dna baser v4
Manufactured by Biosoft
Sourced in Romania
DNA Baser v4.36 is a software application that allows users to assemble and analyze DNA sequences. It provides tools for sequence alignment, annotation, and visualization. The software is designed to assist researchers in tasks related to genomic data processing and analysis.
Automatically generated - may contain errors
4 protocols using dna baser v4
1
Bioinformatic Analysis of Sequencing Data
2
Molecular Identification and Phylogenetic Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The DNA sequences of polymerase chain reaction products were assembled using DNA sequence assembler software DNA Baser v. 4.36 (Heracle BioSoft, Arges, Romania) for contig assembly. The COI gene amplified from H. crudus and the Cicadellidae specimen were aligned in BLASTn (https://blast.ncbi.nlm.nih.gov/) in the National Center for Biotechnology Information, US National Library of Medicine (NCBI) database and the Barcode of Life Database (BOLD). The contigs of the 16S rRNA gene sequences amplified from insects were aligned in BLASTn in the National Center for Biotechnology Information database. The 16S sequences were submitted to National Center for Biotechnology Information GenBank, and were used to build a phylogenetic relationship using maximum likelihood algorithm with boostrap of 1,000 replications in MEGA X (Kumar et al. 2018) with the 16S sequences for all known subgroups of the 16SrIV phytoplasmas, the A subgroup of all known phytoplasma, and with Acholeplasma palmae Tully et al. (Acholeplasmataceae) as an outgroup.
Population survey data were analyzed by the generalized linear model with quasi-poisson distribution. The number of specimens collected between families were analyzed, and multiple comparison Tukey tests was performed to further analyze the significant difference. All statistical tests were performed by using R vers. 3.6.0 (R Core Team 2018).
Population survey data were analyzed by the generalized linear model with quasi-poisson distribution. The number of specimens collected between families were analyzed, and multiple comparison Tukey tests was performed to further analyze the significant difference. All statistical tests were performed by using R vers. 3.6.0 (R Core Team 2018).
3
Metagenomic Discovery of a Fish Polyomavirus
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The RCA DNA (20 µl aliquot from each sample) was sequenced on an Illumina 4000 (Illumina) sequencer at Macrogen (Korea). The paired-end reads were de novo assembled using ABySS v2.02 [29 (link)], and contigs >250 nucleotides were analysed using blast x [30 (link)] against a local viral database. A contig of 372 nucleotides was identified in the liver sample with similarities to VP2 and VP1 of fish PyVs. Based on the sequence of this contig, a pair of abutting primers (F: 5′-CGCTGCTAAAGGAAATAAAATCAAGATATGGGAAT-3′; R: 5′-ACTGGAATTTTAGGCAAATCTATAGCTGACGTTAG-3′) were designed to recover the full genome of this putative PyV. A 0.5 µl sample of the RCA reaction was used as a template for PCR amplification using the abutting primers and Kapa HiFi Hotstart DNA polymerase with the following thermal cycling protocol: 95 °C for 3 min; 25 cycles of 98 °C for 20 s, 60 °C for 15 s, 72 °C for 5 min, and a final extension of 72 °C for 6 min. The amplicon was resolved on a 0.7 % agarose gel, the ~5 kb product was excised, gel-purified and cloned into the pJET1.2 plasmid vector (ThermoFisher, USA). The recombinant plasmid was Sanger-sequenced by primer walking at Macrogen (Korea), and the Sanger sequence contigs were assembled using DNA Baser V4 (Heracle BioSoft S.R.L., Romania).
4
Isolation and Sequencing of TYLCV Genomes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total DNA was extracted from tomato samples displaying leaf curl symptoms from Australia (n ¼52), Iran (n¼ 12) and Mauritius (n ¼6). Circular DNA was enriched by rolling circle amplification (RCA) using Templiphi (GE Healthcare, USA). Unit length TYLCV genomes were recovered from the RCA concatemers using XmnI, NcoI, BamHI or SalI restriction enzymes, and cloned into pJET 1.2 plasmid vector (ThermoFisher, USA) for XmnI digested genomes and into pBluescript SK (Stratagen, USA) for NcoI, BamHI or SalI digested genomes. The recombinant plasmids were Sanger sequenced by primer walking at Macrogen Inc. (South Korea). Complete genome sequences were assembled using DNA Baser V4 (Heracle Biosoft S.R.L., Romania).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!