Sequence Editing

• Sequence Input Wizard 
• Display and edit multiple sequences simultaneously (maximum 100)
• Display complementary strands simultaneously
• RNA Display Mode
• Display the original sequence simultaneously
• Conversion between complementary, opposite, and reverse complementary strands
• 'N' Mask Function
• Sequence Search Function
• Select and connect discontinuous multiple ranges
• Edit Sequence Names
• Modify display font, size, and color
• Import sequences in the following formats: GenBank, multi GenBank, FASTA, multi FASTA, PIR, multi PIR, EMBL, multi EMBL, ABI, SCF, text, and legacy DNASIS 
• Import desired sequences from multiple entry files 
• Open sequences with gaps
• Paste from the Clipboard (automatically eliminates unnecessary character strings)

Annotation Editing

• Automatic recognition and importing of Annotations in GenBank, EMBL and PIR formats.

Trace Data Display/Edit

• Display ABI and SCF trace files
• Delete and edit bases while viewing traces
• Display multiple traces simultaneously
• Adjust display width and height
• Hide/Show specific traces
• Display reverse complementary strands for trace files
• Align relative to referenced sequences (multiple alignment option)
• SNP search (multiple alignment) 

Functions Common to Project Windows

• Show/Hide/Delete sequences
• Change the order in which sequences and analyses are displayed
• Show/Hide/Delete analysis results
• List analysis results
• Set parameters
• Map display:
• Show/hide maps
• Map cursor
• Magnify/Reduce/Full size display
• Copy images to the Clipboard
• Ruler
• Optionally display numbers (and measurement lines) only on top of sequences
• Display numbers on the sides of sequences
• Do not wrap / Wrap by window length / Wrap by set width
• Insert / do not insert spaces between each specified bp/aa

DNA Analysis

• Base Composition
• Codon Frequencies
• GC Content
• Amino Acid Translation
• ORF Search
• Select and edit codon tables; select and edit launch codons
• Add comments to specified ORF
• Hide/show by frame or specified ORF
• Display list of ORFs
• Display DNA sequence for ORF List and Translation predicted sequence
• Printing ORF List
• Restriction Enzyme Site Search
• Display cuts (sequence display) when viewing complementary strands simultaneously
• Display single or multiple restriction enzyme sites simultaneously (map display)
• Search for optimal enzymes to cut out specified ranges
• Specify minimum/maximum number of cut sites
• Up-to-date restriction enzyme database (610 enzymes)
• Display list of restriction enzyme cut sites
• Print list of restriction enzyme cut sites
• Display and print list of predicted fragments
• Mutation Site Search
• Primer Design
• Oligo Probe Design
• Motif Searches:
• Database-specific patterns
• Custom patterns
• Complementary strands
• Display and print motif lists
• Common Motifs
  
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• Trim low quality ends/vectors
• Other Searches:
• Hairpin loops
• Tandem repeats
• Stacking sites

Amino Acid Analysis

• Amino acid composition
• Hydrophilic/Hydrophobic analysis
• Predict isoelectric point (pI)
• Protein assembly enzyme recognition site search
• Motif search
• Common motif search

Database

• Sequence Database
• Search, delete and renew sequences 
• Export to an Editor 
• Vector Database
• Restriction Enzyme Database
• Motif Database
• Protein assembly enzyme recognition site database
• Codon Table