CodonCode Aligner 5.1.5 Leave a comment

Genetics research is a highly complex domain that has greatly benefited from the increase in digital tools. From simple visualization utilities to complex simulators and analyzers, multiple programs have been created to address various issues in this field.
Analyze DNA sequences
Targeting DNA code analyses, mutation detection and sequence assembly, CodonCode Aligner presents itself as a valuable biologist's aid. It can also be employed as a very useful teacher's assistant, as it allows one to view detailed, and informative base traces graphs.
The application can receive samples from various sources, including ABI documents or Chromatogram files; assembly projects can also be loaded and one can even extract data from a valid Genbank ID. Once loaded, users can perform a wide variety of actions upon source samples.
Assemble sequences with cDNA to genomic algorithms
For example, one can assemble sequences using multiple algorithms or remove base ambiguities using automated editing tools. Professional users will also appreciate the program's ability to show the protein translation for every sequence, as well as the mutation detection and analysis feature.
The latter option displays informative charts based on sensitive SNP detection. This is based on heterozygous insertions or deletions analysis algorithms that target both secondary and primary peaks. Once satisfied with their projects, users can export their samples to FASTA files. Other options are available, including transferring assemblies, or consensus sequences, as well as protein translations and features.
The application allows users to perform DNA sequencing analysis, complete with mutations detection
All things considered, CodonCode Aligner is a valuable tool for anyone involved in DNA sequencing and analysis. From simple sequence editing or trimming to complex mapping and phylogenetic tree operations, the program can be a highly useful research tool.

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This software is to analyze the sequences of the DNA (including cDNA) of
Genomic DNA of a living organism and RNA of a living organism. This
software can also analyze the number and sequences of base pairs in a
sequence, insertions and deletions and identify whether there is a SNP
(single nucleotide polymorphism) mutation in a sequence, create an
assembly sequence, and create a new sequence based on a specific region
of a sequence.
• Supports full set of major coding formats (FASTA, FASTQ, FASTQ2,
FASTQ3, FASTQ4, SAM, SAM2, SAM3, CRAM, CRAM2, BAM, BAM2,
BAM3, BAM4, BED, GTF, VCF, VCF2).
• Supports to analyze multiple sequences.
• Supports SAM format.
• Supports BED format.
• Supports GFF and VCF formats.
• Extracts genomic sequences from specified organisms.
• Extracts coding sequences from specified organisms.
• Extracts introns from specified organisms.
• Extracts 5'- and 3'- sequences from specified organisms.
• Extracts polypeptides from specified organisms.
• Supports whole genome sequences.
• Supports complete genome sequences.
• Supports public databases: ENSEMBL, RefSeq, Vega.
• Supports NCBI PubMed and Entrez.
• Supports GEP indexes from Google.
• Supports Chado (dbSNP) and NCBI gene.
• Supports Rfam.
• Supports RepeatMasker.
• Supports BLAST and RepeatMasker.
• Supports BLAST2GO.
• Supports nr, nt, Swissprot, KEGG, COG, GO, TAIR and InterPro.
• Supports gene annotation from various databases.
• Supports gff file.
• Supports VCF file.
• Supports flat file.
• Supports FASTA file.
• Supports FASTQ file.
• Supports FASTQ2 file.
• Supports FASTQ3 file.
• Supports FASTQ4 file.
• Supports SAM file.
• Supports SAM2 file.
• Supports SAM3 file.
• Supports BAM file.
• Supports BAM2 file.
• Supports BAM3 file.
• Supports BAM4 file.
• Supports CRAM file.
• Supports CRAM2 file.
• Supports GTF file.
• Supports VCF file.
• Supports BED file.
• Supports GFF file.
• Supports FASTA file.
• Supports FASTQ file.
• Supports FASTQ2 file.
• Supports FASTQ3 file.
• Supports FASTQ4 file.

● Mac: OS X 10.6.8 or later
● Windows: Windows Vista or Windows 7
● Android: 4.1 or later
● Stable
● 16 MB RAM
● 1024 MB available space
● 500 MB free disk space for installation
● Preferably use network cable to connect to the computer, but also possible to use the USB cable to connect.
● Turn on your computer, choose “Install”
● Mac: Press the “Download” button

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