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CLI Predefined Tasks

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Created by Yuliya Algaer, last modified on Feb 04, 2014

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Using 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 Pattern Using Smith-Waterman Algorithm
Adding Phred Quality Scores to Sequence
Local BLAST Search
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
Annotating with DAS
Gene-by-Gene Report
Reverse-Complement Converting Sequences
Variants Calling
Generating DNA Sequence

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