Extensions

• DNA Annotator
  • Find Group of Annotated Regions
  • Plasmid Auto Annotation
• DNA Flexibility
  • Configuring Dialog Settings
  • Result Annotations
• DNA Statistics
• DNA Generator
• ORF Marker
• Remote BLAST
  • Primer-BLAST
  • Exporting BLAST Results to Alignment
  • Fetching Sequences from Remote Database
• BLAST
  • Creating Database
  • Making Request to Database
  • Fetching Sequences from Local BLAST Database
• Repeat Finder
  • Repeat Finding
  • Tandem Repeats Finding
    • Tandem Repeats Search Result
• Restriction Analysis
  • Selecting Restriction Enzymes
  • Using Custom File with Enzymes
  • Filtering by Number of Hits
  • Excluding Region
  • Circular Molecule
  • Results
• Molecular Cloning in silico
  • Digesting into Fragments
  • Creating Fragment
  • Constructing Molecule
    • Available Fragments
    • Fragments of the New Molecule
    • Changing Fragments Order in the New Molecule
    • Removing Fragment from the New Molecule
    • Editing Fragment Overhangs
    • Adjusting Fragment Ends
    • Reverse Complement a Fragment
    • Other Construction Options
    • Output
  • Creating PCR Product
• In Silico PCR
  • Primers Details
  • Primer Library
• PCR Primer Design for DNA Assembly
  • Backbone Details
• Secondary Structure Prediction
• SITECON
  • SITECON Searching Transcription Factors Binding Sites
  • Types of SITECON Models
    • Eukaryotic
    • Prokaryotic
  • Building SITECON Model
• Smith-Waterman Search
• HMM2
  • Building HMM2 Model
  • Calibrating HMM2 Model
  • Searching Sequence Using HMM2 Profile
• HMM3
  • Building HMM Model
  • Sequence Search Using HMM Profile
  • Searching Sequence Against Sequence Database
• uMUSCLE
  • MUSCLE Aligning
  • Aligning Profile to Profile with MUSCLE
  • Aligning Sequences to Profile with MUSCLE
• ClustalW
• MAFFT
• T-Coffee
• Bowtie
  • Bowtie Aligning Short Reads
  • Building Index for Bowtie
• Bowtie 2
  • Bowtie 2 Aligning Short Reads
  • Building Index for Bowtie 2
• BWA
  • Aligning Short Reads with BWA
  • Building Index for BWA
• BWA-SW
  • Aligning Short Reads with BWA-SW
  • Building Index for BWA-SW
• BWA-MEM
  • Aligning Short Reads with BWA-MEM
  • Building Index for BWA-MEM
• UGENE Genome Aligner
  • Building Index for UGENE Genome Aligner
  • Converting UGENE Assembly Database to SAM Format
  • Map NGS Reads with UGENE Genome Aligner
• CAP3
• SPAdes
• Weight Matrix
  • Searching JASPAR Database
  • Building New Matrix
• Primer3
  • Primer3 (no target sequence)
  • Posterior Actions
  • RTPCR Primer Design
• Spliced Alignment mRNA and cDNA
• External Tools Plugin
  • Configuring External Tool
• ClustalO
• Kalign Aligning
• GeneCut Desktop
• mfold