Aligner v9

Manufactured by CodonCode

Sourced in United States

CodonCode Aligner v9.0.1 is a software application designed for DNA sequence alignment and analysis. It provides tools for comparing and aligning multiple DNA sequences, allowing users to identify similarities and differences between them. The software supports various file formats and offers features for managing, editing, and annotating DNA sequences.

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Lab products found in correlation

Premix d, by Illumina (9 mentions) Taq polymerase, by Merck Group (9 mentions) Simpliamp thermocycler, by Thermo Fisher Scientific (6 mentions) Exosap it express, by Thermo Fisher Scientific (6 mentions) Abi 3130xl genetic analyzer, by Thermo Fisher Scientific (3 mentions) Bigdye terminator v3.1 cycle sequencing kit, by Thermo Fisher Scientific (3 mentions) Bigdye xterminator purification kit, by Thermo Fisher Scientific (3 mentions) Minelute pcr purification kit, by Qiagen (3 mentions) Biospectrometer, by Eppendorf (3 mentions) Abi 3500xl, by Thermo Fisher Scientific (1 mentions)

7 protocols using aligner v9

Genetic Variant Screening for AIS

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Variants appearing in multiple families that were present in the GO functional categories for “cytoskeleton” or “extracellular matrix” (or related terms) were prioritized for genotyping. Additional enrolled affected and unaffected family members were sequenced at the variant site by the Sanger method to establish whether the variant segregated with the AIS phenotype.
PCR was conducted in 20 µL reactions containing 10 µL Premix D (Epicentre Biotechnologies, Madison, WI, USA), 0.2 µL Taq Polymerase (Sigma, St. Louis, MO, USA), 60 ng genomic DNA, and 10 µM Forward and Reverse Primers. PCR reactions were run on a SimpliAmp Thermocycler (Fisher Scientific, Waltham, MA, USA) with a touchdown PCR protocol [38 (link)]. Primer sequences were obtained from Integrated DNA Technologies and are provided in Supplementary Files S2. Sanger sequencing was performed by Quintara Biosciences and chromatograms were analyzed using the CodonCode Aligner v9.0 (CodonCode Corporation, Centerville, MA, USA, https://www.codoncode.com/index.htm (accessed on 16 June 2021)).
Pedigrees for each sequenced family are provided in Supplementary Files S1 and were created using PedigreeXP software (PC Pal, https://www.pedigreexp.com (accessed on 16 June 2021)).

Terhune E.A., Wethey C.I., Cuevas M.T., Monley A.M., Baschal E.E., Bland M.R., Baschal R., Trahan G.D., Taylor M.R., Jones K.L, & Hadley Miller N. (2021). Whole Exome Sequencing of 23 Multigeneration Idiopathic Scoliosis Families Reveals Enrichments in Cytoskeletal Variants, Suggests Highly Polygenic Disease. Genes, 12(6), 922.

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Familial Variant Sanger Sequencing

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DNA from additional affected and unaffected members of the family was Sanger sequenced in order to determine whether the variant segregated with the phenotype. PCR was conducted in 20 μL reactions with 10 μL Premix D (Epicentre Biotechnologies), 0.2 μL Taq Polymerase (Sigma), 20 ng genomic DNA, and 20 μM Forward and Reverse Primers. PCR reactions were run with a touchdown PCR protocol on a SimpliAmp Thermocycler (Fisher Scientific). Protocol and primer sequences are provided in Supp. File S1.
Annealing temperatures were set with the delta function to begin at 65°C and decrease by 0.3 °C each cycle, ending at 55 °C. Primers were obtained from Integrated DNA Technologies. PCR reactions were cleaned up for Sanger sequencing using ExoSAP-IT Express (Thermo Fisher). Sanger sequencing was performed by Quintara Biosciences and chromatograms were analyzed using the CodonCode Aligner v9.0 (CodonCode Corporation, https://www.codoncode.com/index.htm).

Terhune E.A., Cuevas M.T., Monley A.M., Wethey C.I., Chen X., Cattel M.V., Bayrak M.N., Bland M.R., Sutphin B., Trahan G.D., Taylor M.R., Niswander L.A., Jones K.L., Baschal E.E., Antunes L., Dobbs M., Gurnett C., Appel B., Gray R, & Miller N.H. (2020). Mutations in KIF7 Implicated in Idiopathic Scoliosis in Humans and Axial Curvatures in Zebrafish. Human mutation.

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Family-based Sanger Sequencing of Exome Variants

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DNA from additional affected and unaffected family members was Sanger sequenced across the variants of interest detected through exome sequencing. Primers were designed using Primer3 and obtained from Integrated DNA Technologies. PCR was conducted in 20 µL reactions with 10 µL Premix D (Epicentre Biotechnologies), 0.2 µL Taq Polymerase (Sigma), 20 ng genomic DNA, and 20 µM Forward and Reverse Primers. PCR reactions were run with a touchdown PCR protocol on a SimpliAmp Thermocycler (Fisher Scienti c). Annealing temperatures were set with the delta function to begin at 65°C and decrease by 0.3 °C each cycle, ending at 55 °C. PCR reactions were cleaned up for Sanger sequencing using ExoSAP-IT Express (Thermo Fisher). Sanger sequencing was performed by Quintara Biosciences and chromatograms were analyzed using the CodonCode Aligner v9.0 (CodonCode Corporation, https://www.codoncode.com/index.htm).

Wang Y., Liu Z., Yang G., Troutwine B., Gao Y., Chen H., Xiao L., Li J., Terune E., Wethey C.I., Guo C., Tang M., Miller N., Xu S., Xie L., Zhang H., & Gray R.S. (2020). Rare coding variants in axonemal dynein heavy chain genes are associated with adolescent idiopathic scoliosis.

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RBMX Variant Amplification and Sequencing

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DNA was extracted from peripheral blood from 36 individuals in the extended pedigree (Fig. 1A and Supplementary Table 1). The region spanning the RBMX variant (NM_002139.4; c.484_486del, p.(Pro162del)) was amplified using 20–50 ng DNA, the RBMX_DNA primers and PCR protocol described in Supplementary material 1. Cycle sequencing was then performed using BigDye Terminator v3.1 Cycle Sequencing kit (Thermo Fisher Scientific, Carlsbad, CA, USA) according to manufacturer’s instructions with cycling parameters: 96°C 1 min, 30x (96°C 10 s, 50°C 5 s, 60°C 30 s) 4 °C hold. All samples were cleaned up using BigDye XTerminator Purification kit (Thermo Fisher Scientific, Bedford, MA, USA) and capillary electrophoresis was performed on 3130XL ABI Genetic Analyzer (Thermo Fisher Scientific, Foster City, CA, USA). The result was analyzed using CodonCode Aligner v9.0.1 (CodonCode Corporation, www.codoncode.com).

Johansson J., Lidéus S., Frykholm C., Gunnarsson C., Mihalic F., Gudmundsson S., Ekvall S., Molin A.M., Pham M., Vihinen M., Lagerstedt-Robinson K., Nordgren A., Jemth P., Ameur A., Annerén G., Wilbe M, & Bondeson M.L. (2023). Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions. European Journal of Human Genetics, 32(3), 333-341.

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DNA Isolation and Mitochondrial D-loop Sequencing

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Genomic DNA was isolated using a commercial kit (GSure Blood DNA Mini Kit, GCC Biotech India Pvt. Ltd, Kolkata, India, Cat. No. G4626), following the manufacturer’s instructions. The quality and concentration of isolated DNA samples were checked using a BioSpectrometer (Eppendorf, Hamburg, Germany) and DNA samples were then stored at -20°C until further use. Complete mitochondrial D-loop was amplified using the primers and PCR conditions described earlier by Yang et al. [34 (link)]. Amplified products were purified by using MinElute PCR Purification Kit, Qiagen, Cat. No. 28004 (New Delhi, India) and sequenced in both directions by Sanger dideoxy fingerprinting. The generated sequences were edited using Codon code Aligner v 9.0.1 (CodonCode Corporation, www.codoncode.com).

De A.K., Sawhney S., Muthiyan R., Bhattacharya D., Ponraj P., Malakar D., Sunder J., Sujatha T., Kumar A., Mondal S., Bera A.K., Bala P.A, & Chakurkar E.B. (2022). Legacies of domestication, Neolithic diffusion and trade between Indian subcontinent and Island Southeast Asia shape maternal genetic diversity of Andaman cattle. PLOS ONE, 17(12), e0278681.

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Comparative Analysis of HBV Genome Sequences

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In total, 146 human HBV genome sequences from 10 acute hepatitis B (AHB) patients and 150 sequences from 10 chronic hepatitis B (CHB) patients, previously established as nonrecombinant, were selected [21 (link)]. B56 as a reference sequence was compared with 1061 HBV full-length genotype B sequences from NCBI GenBank to identify variations at the nucleotide level. Sequencing quality and data manipulations were analyzed using Codon Code Aligner v9.0.1 (CodonCode Corporation, Dedham, MA, USA).

Lin J., Li J., Xie P., Han Y., Yu D., Chen J, & Zhang X. (2021). Hepatitis B virus middle surface antigen loss promotes clinical variant persistence in mouse models. Virulence, 12(1), 2868-2882.

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Molecular Detection of Antibiotic Resistance Genes

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The third-generation cephalosporin- and carbapenem-resistant isolates were screened for the presence of genes encoding ESBLs (bla_CTX-M, bla_TEM, bla_SHV) and carbapenemases (bla_OXA-48, bla_VIM, bla_IMP, bla_NDM and bla_KPC), using the quantitative real-time PCR (qPCR) as previously described [26 (link)]. The qPCR positive isolates were confirmed by conventional PCR. The genetic variant of the carbapenemase genes was determined by sequencing of the positive PCR amplicons in both directions using the same set of standard PCR primers with BigDye Terminator on an automated ABI 3500XL genetic analyser (Applied Biosystems, Foster City, CA, USA) according to the previously described protocol [27 ]. The generated raw-read sequences were assembled using codon code aligner, v 9.0.1 (Codon Code Corp., Centerville, MA, USA). The assembled sequences were identified by Blast analysis against the ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation) database [28 (link)].

Olowo-okere A., Ibrahim Y.K., Olayinka B.O., Ehinmidu J.O., Mohammed Y., Nabti L.Z., Rolain J.M, & Diene S.M. (2020). Phenotypic and genotypic characterization of clinical carbapenem-resistant Enterobacteriaceae isolates from Sokoto, northwest Nigeria. New Microbes and New Infections, 37, 100727.

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