DNASIS MAX Analysis Tools

Homology Search

• Internet Blast Search
• Local Blast Search
• Smith-Waterman Search
• Homology Search Viewer

Multiple Alignment

• Multiple Alignment(ClustalW)
• Graphical View
• Create phylogenetic tree (Neighbor-Joining Method)
• Phylogenetic tree Viewer

Restriction Enzyme Site Search

• Display cut sites (sequence display) on both strands
• Display restriction enzyme sites individually or all at once (map display)
• Find enzymes to cut out specified ranges
• Specify minimum/maximum number of cut sites
• Up-to-date restriction enzyme database (610 enzymes)
• Display and print list of restriction enzyme cut sites
• Display and print list of predicted fragments

Primer / Oligo Probe Design

• Primer design using Primer3
• Primer design for Real-Time PCR
  • Design primers for SYBR Green assays
  • Design primers and probes for  TaqMan® Probe assays
• Oligo Probe Design

siRNA Design

• Design siRNAs based on established practices
• Evaluate sequence specificity of siRNA with BLAST of NCBI database or in-house sequence databases
• Graphical Results View enables quick and easy analysis

Other Features

• Base Composition
• Codon Frequencies
• GC Content
• Amino Acid Translation
• ORF Search:
  • Select and edit codon tables and start codons
  • Add comments to specified ORFs
  • Hide/show individual ORFs or entire frames
  • Display and print list of ORFs with both DNA and predicted amino acid sequences
• Mutation Site Search
• Motif Search:
  • Database specific pattern searches
  • Custom patterns
  • Search complementary strands
  • Display and print list of motifs
  • Find common motifs
• Trim low quality ends and vector sequences
• 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