Aligner version 3
CodonCode Aligner version 3.7.1 is a software application designed for sequence alignment and analysis. It provides tools for comparing and aligning DNA, RNA, and protein sequences.
Lab products found in correlation
10 protocols using aligner version 3
Mitochondrial DNA Barcoding of Fish
Mitochondrial DNA Barcoding of Fish
Mitochondrial DNA Sequencing of Fish
Mitochondrial DNA Barcoding Protocol
Mitochondrial COI Gene Sequencing Protocol
Mitochondrial DNA Barcoding for Species ID
as per the manufacturer's instructions. The 5 ʹ region of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was amplified with the primers FishF1 (5 ʹ -TCA ACC AAC CAC AAA GAC ATT GGC AC-3 ʹ ) and FishR1 (5 ʹ -TAG ACT TCT GGG TGG CCA AAG AAT CA-3 ʹ ) (Ward et al., 2005) . PCR reactions were performed in a total volume of 20 µl, containing 1 ng of DNA, 1× CoralLoad PCR buffer, 3 mM MgCl 2 , 66 µM of each dNTP, 0.15 µM of each primer and 0.5 units of Taq DNA polymerase (Qiagen). The amplification protocol was 4 min at 94°C, followed by 40 cycles at 94°C for 30 s, 48°C for 40 s, and 72°C for 50 s, with a final extension step at 72°C for 7 min. PCR products were purified (Ampure XP Kit, Beckman Coulter, Brea, USA) and sequenced in both directions on a 3730xl DNA Analyzer 96-capillary sequencer (Applied Biosystems, Foster City, USA). We used CodonCode Aligner version 3.7.1 software (CodonCode Corporation, Dedham, MA, USA) to edit the sequence, which was 652 bp in length, compared it to the GenBank database content with BLAST, and deposited it in GenBank under the accession number MK275650. Species identification was confirmed with the BOLD identification engine (Ratnasingham & Hebert, 2007) .
DNA Barcoding of Fish Species
Metabarcoding of Fish Mitochondrial COI Gene
PCR products were purified (Ampure XP Kit, Beckman Coulter) and sequenced in both directions on a 3730xl DNA Analyzer 96-capillary sequencer (Applied Biosystems). We used CodonCode Aligner version 3.7.1 software (CodonCode Corporation, Dedham, MA, USA) to edit sequences, which were 652 bp in length, compared them to the GenBank database content with BLAST, and deposited them in GenBank under accession numbers KX926437 -KX926442. Species identification was confirmed with the BOLD identification engine [20] .
Molecular Profiling of Microbial Communities
HLA-G Allele Typing by PCR and Sequencing
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