Key Features for DNA Sequence Analysis in CodonCode Aligner

CodonCode Aligner offers intuitive, user-friendly tools for DNA sequence assembly, pairwise and multi-sequence alignment, Sanger chromatogram editing, mutation analysis, and other key workflows in molecular biology research, including:

Import and Export

• Import Sanger sequence chromatograms in ABI, AB1, or SCF format
• Import text files in GenBank, FASTA, FASTQ, Sam, .dna, or EMBL format
• Import a subset of samples (e.g. every nth sample, or only samples matching selected sequences in your project)
• Create new text sequences using copy and paste
• Import from GenBank by accession number
• Export sequences, consensus sequences, alignments, protein translations to SCF, FASTA, FASTQ, NEXUS/PAUP or Phylip

Sequence Editing and Trimming

• Manual editing of sequences and contigs, including delete to sample or contig end and contig splitting
• Automated editing tools: call or remove ambiguities, match consensus, convert low quality bases to N, undo auto-edits
• Trace sharpening for poor quality regions in Sanger chromatograms
• Fast navigation with toolbar buttons or keyboard shortcuts; user-definable regions of interest
• End clip to remove low quality sequence; remove vector contamination

Sequence Assembly

• Assemble fragments using local, end-to-end, or large gap (cDNA to genomic) algorithms
• Accurate, quality based consensus sequences minimize the need for manual editing
• Automatically assemble many clones using "Assemble by name"
• Assemble and scaffold bacterial genomes from NGS sequences

Sequence Alignment

• Create pairwise and multi-sequence alignments with MUSCLE, Clustal Omega, or built-in algorithms
• Align to reference sequences
• Align cDNA to genomic DNA
• Build "contigs of contigs": align contigs to each other directly
• Go back from the contig alignment to the original traces with a double-click
• Edit the sequence traces, the contig view, or the alignment of contigs, while keeping your data consistency
• Create Bowtie2 alignments for NGS reads, and display paired ends

Sequence Translation

• Show the protein translation for every sequence
• Switch back and forth between showing amino acids and bases
• See translation-based background colors
• Show the protein translation of your consensus sequences for annotated coding regions

Virtual Cloning

• Simulate your Restriction Cloning operations, easily finding matching overhangs for vector and insert
• Virtual Gibson Assembly with up to 15 fragments
• Blunt end PCR and TOPO cloning
• Directional TOPO cloning
• TA cloning
• Automatically pick cloning primers
• Manually edit primers to insert e.g. spacers or to adjust the reading frame
• Export primers directly during your experiment
• Verify your clone by looking at the reading frame

Restriction Mapping

• Build restriction maps using any combination of restriction enzymes
• Select by size of recognition site, overhang, cut frequency, of manufacturer
• View as single-line or multi-line maps, as text, or as virtual gel
• Select restriction fragments by clicks on restriction maps for copying

RFLP Analysis

• Automatically identify restriction enzymes that produce different gel lanes
• Compare cut sites for samples in a contig
• See and print the expected virtual gel, fragment lengths for each enzyme, or aligned samples with cut sites

Primer Design

• Design PCR and sequencing primers
• Create PCR primers at fixed locations for cloning
• Primers are highlighted in your template sequence for easy recognition
• Each primer can be imported in your project with detailed primer information
• Export primers for ordering

Phylogenetic Trees

• Build Neighbor-Joining trees for your contigs
• Build trees for selected bases only to sort your samples by differences in a specific region
• Split contigs by trees

Mutation Detection and Analysis

• Call secondary peaks in sequence traces
• Sensitive detection of heterozygous SNPs in assembled or aligned contigs
• View and export amino-acid level effects of mutations
• Accurate and sensitive detection of heterozygous insertions and deletions
• Split heterozygous indels into shorter and longer pseudo-alleles
• Subtract wild type traces to reveal mutated alleles

Difference Tables

• Spot differences in your contigs by using the difference tables
• Verify the differences by clicking on a cell in the difference table to navigate to a difference in the contig
• Get an overview of all differences by looking at the condensed version of the difference table
• Only look at differences that interest you by using filters
• Export differences

Customization

• Color bases by nucleotide, sequence quality, or amino acid translation
• Hide bases that match the consensus sequence
• Choose toolbar buttons and buttons styles
• Fine-tune settings through extensive preferences
• Lock, save, or load preference files
• Use scripts to automate repetitive tasks

Methylation Analysis

• Analyze methylation of cytosines after bisulfite modification, PCR, and capillary sequencing from ABI data
• View "raw" ABI trace data
• Methylation analysis uses raw trace data, thereby avoiding artifacts from trace "normalization"
• Get methylation results for individual sequences as well as the observed range for a contig base

 

This is only a partial list of features. To see what CodonCode Aligner can do, download the free trial version and use CodonCode Aligner with your own data.