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Seqman 2 program

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SeqMan II is a DNA sequence assembly and analysis software program developed by DNASTAR. Its core function is to accurately assemble and analyze DNA sequences from multiple sources.

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Lab products found in correlation

Abi prism 3100 dna sequencer, by Thermo Fisher Scientific (4 mentions) Pmd19 t vector system, by Takara Bio (1 mentions) Trizol, by Thermo Fisher Scientific (1 mentions) Primescript rt reagent kit, by Takara Bio (1 mentions) Du800, by Beckman Coulter (1 mentions) Tianamp blood dna kit, by Tiangen Biotech (1 mentions)

6 protocols using seqman 2 program

1

Comprehensive Genome Sequencing of IBV Strains

Cited 1 time
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Total RNA was extracted from virus-infected allantoic fluid using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. cDNA was generated using the PrimeScript RT reagent Kit (Takara Bio Inc., Shiga, Japan) following the supplier's guidelines. The primers and strategies used for cloning the complete and 3′/5′ termini of IBV strains were as previously described (Wu et al., 2016 (link)). Where primers did not work due to sequence differences, new primers were designed based on newly determined sequences flanking those genome regions. Each PCR amplicon was cloned into a PMD-19 T vector system (Takara Bio Inc.), and 3 to 5 independent clones were sequenced for each amplicon. Each nucleotide was determined from at least 3 identical results generated from separate PCR products. The nucleotide sequences of the positive clones, determined by Sangon Biological Engineering Technology (Shanghai, China), were then assembled into complete genome sequence using SeqMan II program of DNAstar software package (DNAStar, Madison, WI).
Yan W., Qiu R., Wang F., Fu X., Li H., Cui P., Zhai Y., Li C., Zhang L., Gu K., Zuo L., Lei C., Wang H, & Yang X. (2021). Genetic and pathogenic characterization of a novel recombinant avian infectious bronchitis virus derived from GI-1, GI-13, GI-28, and GI-19 strains in Southwestern China. Poultry Science, 100(7), 101210.
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2

PCR Amplicon Sequencing Protocol

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PCR was carried out using the standard protocol (Qiagen, Germantown, MD, USA). The PCR products were treated with the shrimp alkaline phosphatase and exonuclease-I to degrade deoxynucleotide triphosphates and unincorporated PCR primers. The purified amplicons were mixed with 10 picomoles of the forward and reverse PCR primers for bidirectional sequencing on an ABI-Prism 3100 DNA sequencer via dye termination chemistry (Applied Biosystems, Foster City, CA, USA). DNA sequence variants were identified using the SeqMan II program (DNA-STAR Inc., WI, USA).
Wang H., Wang X., He C., Li H., Qing J., Grati M., Hu Z., Li J., Hu Y., Xia K., Mei L., Wang X., Yu J., Chen H., Jiang L., Liu Y., Men M., Zhang H., Guan L., Xiao J., Zhang J., Liu X, & Feng Y. (2015). Exome Sequencing Identifies a Novel CEACAM16 Mutation Associated with Autosomal Dominant Nonsyndromic Hearing Loss DFNA4B in a Chinese Family. Journal of human genetics, 60(3), 119-126.
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3

PCR Amplicon Sequencing Protocol

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PCR was carried out using the standard protocol (Qiagen, Germantown, MD, USA). The PCR products were treated with the shrimp alkaline phosphatase and exonuclease-I to degrade deoxynucleotide triphosphates and unincorporated PCR primers. The purified amplicons were mixed with 10 picomoles of the forward and reverse PCR primers for bidirectional sequencing on an ABI-Prism 3100 DNA sequencer via dye termination chemistry (Applied Biosystems, Foster City, CA, USA). DNA sequence variants were identified using the SeqMan II program (DNA-STAR Inc., WI, USA).
Wang H., Wang X., He C., Li H., Qing J., Grati M., Hu Z., Li J., Hu Y., Xia K., Mei L., Wang X., Yu J., Chen H., Jiang L., Liu Y., Men M., Zhang H., Guan L., Xiao J., Zhang J., Liu X, & Feng Y. (2015). Exome Sequencing Identifies a Novel CEACAM16 Mutation Associated with Autosomal Dominant Nonsyndromic Hearing Loss DFNA4B in a Chinese Family. Journal of human genetics, 60(3), 119-126.
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4

Genetic Screening for Waardenburg Syndrome

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Genomic DNA was extracted from the peripheral blood cells of subjects and healthy controls using the phenol/chloroform method. We performed PCR Sanger sequencing on all coding exons and flanking intronic sequences of WS2-associated MITF (OMIM #156845) and SNAI2 (OMIM #602150). PCR was carried out using the standard protocol (Qiagen, Germantown, MD, USA). The PCR products were treated with the shrimp alkaline phosphatase and exonuclease-I to degrade deoxynucleotide triphosphates and unincorporated PCR primers. The purified amplicons were mixed with 10 picomoles of the forward and reverse PCR primers for bidirectional sequencing on an ABI-Prism 3100 DNA sequencer via dye termination chemistry (Applied Biosystems, Foster City, CA, USA). SeqMan II program (DNA-STAR, Madison, WI, USA) was used to compare results. DNA samples from the controls were further screened for the same mutation.
Sun J., Hao Z., Luo H., He C., Mei L., Liu Y., Wang X., Niu Z., Chen H., Li J.D, & Feng Y. (2017). Functional analysis of a nonstop mutation in MITF gene identified in a patient with Waardenburg syndrome type 2. Journal of Human Genetics, 62(7), 703-709.
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5

Mitochondrial Genome Sequence Analysis

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Sequence annotation was performed using blast tools available from the NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi), and SeqMan II program from the Lasergene software package (DNASTAR Inc.; Madison, USA). The protein-coding sequences were translated into putative proteins on the basis of the Invertebrate Mitochondrial Genetic Code. The skewness was measured by the method given by Junqueiraet al.[12 (link)], and the base composition of nucleotide sequences were described as: AT skew = [A−T]/[A+T], GC skew = [G−C]/[G+C]. The relative synonymous codon usage (RSCU) values were calculated using MEGA 5.1[13 (link)].
The tRNA genes were determined using the tRNAscan-SE software (http://lowelab.ucsc.edu/tRNAscan-SE/) [14 (link)], or predicted by sequence features of being capable of folding into the typical cloverleaf secondary structure with legitimate anticodon. The tandem repeats in the A+T-rich region were determined by the tandem repeats finder program (http://tandem.bu.edu/trf/trf.html)[15 (link)].
Sun Y., Chen C., Gao J., Abbas M.N., Kausar S., Qian C., Wang L., Wei G., Zhu B.J, & Liu C.L. (2017). Comparative mitochondrial genome analysis of Daphnis nerii and other lepidopteran insects reveals conserved mitochondrial genome organization and phylogenetic relationships. PLoS ONE, 12(6), e0178773.
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6

Molecular Genetic Screening for Waardenburg Syndrome

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Genomic DNA was removed from peripheral blood samples of the subjects and healthy controls according to the standard procedure. Whole genomic DNA was isolated with a TIANamp Blood DNA Kit (Tiangen Biotech, China.) and quantified with an ultraviolet spectrophotometer Du800 (Beckman Coulter, United States). The DNA was then kept at –20°C until use. PCR and Sanger sequencing was conducted on each of the coding exons and flanking splicing sites of the WS-related genes, including MITF, SOX10, PAX3, EDNRB, EDN3, and SNAI2. The PCR products were treated with shrimp alkaline phosphatase and exonuclease-I to degrade deoxynucleotide triphosphates and unincorporated PCR primers. The purified amplicons were combined with 10 picomoles of the forward and reverse PCR primers for bidirectional sequencing on an ABI-Prism 3100 DNA sequencer via dye-termination chemistry (Applied Biosystems, United States), and the SeqMan II program (DNA-STAR, United States) was utilized to compare results. Once the mutation was determined, DNA samples from related family members and controls were then screened for the identical mutation.
Wen J., Song J., Bai Y., Liu Y., Cai X., Mei L., Ma L., He C, & Feng Y. (2021). A Model of Waardenburg Syndrome Using Patient-Derived iPSCs With a SOX10 Mutation Displays Compromised Maturation and Function of the Neural Crest That Involves Inner Ear Development. Frontiers in Cell and Developmental Biology, 9, 720858.
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