CLI Predefined Tasks

With the current version of UGENE, you can perform the following tasks by running a simple command:

• Format Converting Sequences
• Converting MSA
• Extracting Sequence
• Finding ORFs
• Finding Repeats
• Finding Patterns Using the Smith-Waterman Algorithm
• Adding Phred Quality Scores to Sequence
• Local BLAST Search
• Remote NCBI BLAST and CDD Requests
• Annotating Sequence with UQL Schema
• Building Profile HMM Using HMMER2
• Searching HMM Signals Using HMMER2
• Aligning with MUSCLE
• Aligning with ClustalW
• Aligning with ClustalO
• Aligning with Kalign
• Aligning with MAFFT
• Aligning with T-Coffee
• Building PFM
• Searching for TFBS with PFM
• Building PWM
• Searching for TFBS with Weight Matrices
• Building Statistical Profile for SITECON
• Searching for TFBS with SITECON
• Fetching Sequence from Remote Database
• Gene-by-Gene Report
• Reverse-Complement Converting Sequences
• Variants Calling
• Generating DNA Sequence