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Extensions

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Created by Yuliya Algaer, last modified by Ivan Protsyuk on Nov 20, 2014

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Workflow Designer
DNA Annotator
DNA Flexibility
Configuring Dialog Settings
Result Annotations
DNA Statistics
DNA Generator
ORF Marker
Remote BLAST
Exporting BLAST Results to Alignment
Fetching Sequences from Remote Database
BLAST/BLAST+
Creating Database
Making Request to Database
Fetching Sequences from Local BLAST Database
Repeat Finder
Repeats 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
Reverse Complement a Fragment
Other Constuction Options
Output
Creating PCR Product
In Silico PCR
Primers Details
Primer Library
Secondary Structure Prediction
SITECON
SITECON Searching Transcription Factors Binding Sites
Types of SITECON Models
Eukaryotic
Prokaryotic
Building SITECON Model
Smith-Waterman Search
HMM2
Building HMM Model (HMM Build)
Calibrating HMM Model (HMM Calibrate)
Searching Sequence Using HMM Profile (HMM Search)
HMM3
Building HMM Model (HMM3 Build)
Searching Sequence Using HMM Profile (HMM3 Search)
Searching Sequence Against Sequence Database (Phmmer Search)
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
Aligning Short Reads with UGENE Genome Aligner
Building Index for UGENE Genome Aligner
Converting UGENE Assembly Database to SAM Format
CAP3
SPAdes
Weight Matrix
Searching JASPAR Database
Building New Matrix
Primer3
RTPCR Primer Design
Spliced Alignment (mRNA to genomic)
External Tools
Configuring External Tool
Query Designer
Plasmid Auto Annotation
ClustalO
Kalign Aligning

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