The amplified sequences were spliced using SeqMan tool from the DNASTAR package (DNASTAR, Inc., Madison, WI, USA). Multiple sequence alignment was carried out for nucleotide and amino acid sequence using the optimal alignment tool in the DNAMAN software package (Lynnon, Biosoft, Canada). Phylogenetic tree performed by a maximum likelihood method with MEGA 7.1 software and ORF finder was used to predict the amino acid sequence encoded by nucleotides.
Seqman tool
Manufactured by DNASTAR
Sourced in United States
SeqMan is a DNA sequence assembly tool that allows users to assemble, edit, and analyze DNA sequences. It provides a comprehensive set of tools for sequence assembly, editing, and analysis, enabling researchers to efficiently process and manage their DNA sequencing data.
Automatically generated - may contain errors
Lab products found in correlation
Fastdigest ecori, by Thermo Fisher Scientific (1 mentions)
Pgem t easy vector, by Promega (1 mentions)
Favorprep gel pcr purification kit, by Favorgen Biotech (1 mentions)
Abi 3100 capillary sequencer, by Thermo Fisher Scientific (1 mentions)
Abi prism 3130xl genetic analyzer, by Thermo Fisher Scientific (1 mentions)
Coffalyser software, by MRC-Holland (1 mentions)
Software, by DNASTAR (1 mentions)
5 protocols using seqman tool
1
Phylogenetic Analysis of Amplified Sequences
2
Genome Walking for Full-length phaC DNA
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Genome walking with inverse affinity nested PCR (IAN-PCR) was carried out to obtain the full-length phaC DNA sequences [61 (link)]. WGA seawater DNA was digested with FastDigest EcoRI (Fermentas, Lithuania) and self-ligated using a DNA Ligation Kit Ver1.2 (TaKaRa, Japan). For each genetic group, two sets of primers (for two rounds of amplification) (Additional file 6 : Table S1) were designed based on the partial phaC sequences obtained in the previous step. The first round of amplification (inverse affinity PCR) included a 5′-biotinylated primer that enabled the product to be purified using the KiloBase Binder Kit (Invitrogen, USA) and serve as a template for the second round of amplification (nested PCR). DNA sequences were determined by performing the same cloning and sequencing steps described in the previous section. Full-length phaC sequences were predicted in silico by assembling the genome walking DNA fragments using the SeqMan tool (DNASTAR, USA).
3
Characterization of FaOMT Promoter Fragments
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For characterization of the FaOMT promoter fragment from selected strawberry accessions, PCR and separation in agarose electrophoresis were performed as previously described for FaOMT-SI/NO marker test. Selected bands of about 500 bp from F. virginiana UC-11 and F. moschata ‘Capron Royale’, and 248 bp from F. × ananassa cv. ‘Aromas’, ‘Candonga’, ‘Elvira’, and ‘Pedrone’ were isolated and purified from the agarose gel using the FavorPrep GEL/PCR purification kit (Favorgen Biotech Corp.) and cloned into the pGEM-T Easy vector (Promega). Five independent clones were sequenced for each of the three accessions and assembled into individual contigs using the SeqMan tool (DNAStar). Sequence analyses and comparisons were carried out using the Lasergen software (DNAStar) and the tool Clustal W2 from EBI-EMBL.
4
Variant Verification in PALB2 and CHEK2 Genes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA variants, including single-nucleotide variants (SNPs), small ins/del, and CNVs, identified through the method tested in the current study in the PALB2 and CHEK2 genes, were further verified using a second independent molecular technique. Specifically, PCR-specific amplification followed by Sanger sequencing was performed for point variants and/or small ins/del. After amplicon verification on a 2% agarose gel, sequencing was carried out using an ABI 3100 capillary sequencer (Applied Biosystems Inc., Foster City, CA, USA). The obtained electropherograms were analyzed using the SeqMan tool (DNASTAR, Inc., Madison, WI, USA). For CNV validation, multiplex ligation probe amplification (MLPA) was carried out using gene-specific SALSA MLPA probe sets (MRC-Holland, Amsterdam, the Netherlands) and an ABI PRISM 3130 XL genetic analyzer (Applied Biosystems Inc., Foster City, CA, USA) for fragment separation. Finally, the Coffalyser software (MRC-Holland, Amsterdam, the Netherlands) was used for MLPA results analysis, according to the manufacturer’s instructions.
5
Phylogenetic Analysis of Genome Sequences
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The nucleotide sequences were systematically aligned and scrutinized using the SeqMan tool integrated within the DNAStar software package (DNAStar Inc., United States; Deng et al., 2015 (link); Kumar et al., 2018 (link)). Phylogenetic reconstruction of the 5’-UTR and complete genome sequences was performed using the neighbor-joining method in MEGA 7.0 software (Tamura et al., 2004 (link)). The statistical robustness of the phylogenetic tree was assessed by bootstrapping the data set with 1,000 replicates.
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!