Tutorial: Alignment of Short Reads with UGENE In this block we will perform short reads alignment using UGENE. One of the applications of alignment is the gene mapping. We will do genomic mapping of a simulated dataset generated from E.coli reference genome (NC_010473). The dataset consists of 100,000 paired-end reads of size 50 bp. Starting more…

UGENE Mini-Tutorials: Open Databases, Genome Mapping and More Separate a set of primer sequences How to separate a set of primer sequences into compatible groups? If you want to do a set of PCR reactions for amplifying of several sequences (e.g. for extracting of a set of genes), you can save your time and money more…

UGENE 1.15 List of Features This article is a brief overview of the UGENE 1.15 new features. We have improved the UGENE’s ability of working with shared databases. It is possible now to use the databases in your workflows. Workflows can use databases in both ways: read data from a database and write data to more…

Tutorial: Building Phylogenetic Trees in UGENE This tutorial is about phylogenetic trees building methods available in the UGENE platform. So here UGENE is presented as a phylogenetic tree maker. UGENE allows you to visualize, edit and build phylogenetic trees and phylogenetic relationship. You can also connect it to your multiple alignment and edit the tree with more…

UGENE Mini-Tutorials: Consensus Sequence, Filter Sequences by Phred Quality Score and More Generating DNA Sequence If you need to get a set of sequences, for example, for testing your genome analysis algorithm, UGENE will help you with it. Just run UGENE via the command-line interface: ugene –task=generate-dna –count= –length= –out= In addition, you can set other options of more…

UGENE Tips: GC Content, Export Consensus and more Graphs Did you know that you can plot different kinds of statistical graphs based upon your sequences in UGENE? To view available graph types click the "Graphs" button on the sequence editor toolbar. Then choose the required one from the popup list, for example, "GC Content" or more…

UGENE Mini-Tutorials: DNA Reverse Complement, Find Repeats and More How to get a DNA reverse complement sequence UGENE Workflow Designer is a very effective and convenient system for running calculations with whole datasets, not only with a single sequence or alignment. For example, you can use it for getting DNA reverse complement sequences for a set more…

UGENE Tips: Multiple Sequence Alignment Colors, Dot Plots and more Multiple Alignment Highlighting Did you know how to make a multiple alignment more illustrative with UGENE? It's often needed to evaluate similarity or difference between one sequence and the others. Specially for this purpose the UGENE Multiple Alignment Editor allows specifying a reference sequence that more…

Tutorial: NCBI BLAST Search Feature of UGENE Workflow Designer. BLAST search against NCBI probably one of the most popular features in bioinformatics. There are many services, including NCBI itself for BLAST search. This tutorial presents the UGENE version of BLAST search. If you have multiple sequences to do a BLAST search probably you do not more…

UGENE Mini-Tutorials: Workflow Designer Samples and Inverted Repeats and More Workflow Designer samples UGENE Workflow Designer provides the set of ready-to-use samples. Each sample solves a particular bioinformatics task. The list of the samples is available in the “Samples” tab of the Workflow Designer window. A mouse click on a sample shows the information block more…