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March 31st, 2015 : PCR in silico

pcr in silico

Tutorial: UGENE PCR in silico PCR primer designing is a day to day lab activity. Also you might want to check if a designed primer that your lab uses is applicable to your new sequence. By checking your primer (e.g. melting temperature of primers or primer hairpin) with in silico PCR features you can track more…



March 31st, 2015 : Multiple Sequence Alignment Overview

UGENE Multiple Sequence Alignment Overview

Tutorial: UGENE Multiple Alignment Overview Multiple Alignment Editor has many features common to multiple sequence alignment tools like highlighting of diffidences to spot mutations, finding a subsequence in an alignment and gap removing. But sometimes you want to see the alignment as a whole, that is where the overview might help, this is one of the more…



March 12th, 2015 : Public Databases

UGENE Public Database

UGENE Tips: Public Databases UGENE Public Database Next time you need mouse, drosophila or arabidopsis chromosome sequences don't be in a hurry to go to the NCBI site since UGENE has embedded access to annotated sequences of often used genomes including human, HIV, zebrafish and a few others. Almost a year ago we created a public more…



February 20th, 2015 : UGENE 1.16

snpeff pipeline

UGENE 1.16 List of Features This article is a brief overview of the UGENE 1.16 new features. We made the data search in UGENE more comfortable. It is possible now to search different kinds of data in your project. Generic Search Just write a string you want to search for and it will be found more…



February 14th, 2015 : ​Shared Databases in UGENE

Shared Database in UGENE

Tutorial: Shared Databases in UGENE Do you need to share data, such as sequences, with your colleagues in a lab? How to create a plasmid database, gene database or a genome sequence database? From this tutorial you will learn how you can easily do it with UGENE. You can easily share sequences, annotated sequence, multiple more…



February 5th, 2015 : Amino-translations and Identical Sequences

Amino-translation

UGENE Tips: Amino-translations, Identical Sequences and more Amino-translation Did you know how to get quickly a multiple amino-translation of DNA alignment in UGENE? To do this open a needed file with a multiple DNA alignment by UGENE. Then open a right-click menu and select { Export -> Amino translation… }. After that a dialog appears more…



February 2nd, 2015 : SNP Search and SNP Effect

UGENE Story

UGENE Mini-Tutorials: SNP Search, SNP Effect and More UGENE Story A story about how UGENE Workflow Designer and the team helped a user. Last week a user sent us an e-mail to ugene@unipro.ru. He tried to solve a task with UGENE and he did not understand how to do it. The task was the following: The more…



January 29th, 2015 : Pairwise Alignment and Remove Gaps

Pairwise Alignment

UGENE Tips: Pairwise Alignment, Remove Gaps and more Pairwise Alignment Did you know how to build quickly a pairwise alignment for sequences included to a multiple alignment? To do this you need to open the "Pairwise Alignment" tab in the Alignment Editor Options Panel and specify two sequences there. The following algorithms are available for more…



January 16th, 2015 : NGS Pipelines in UGENE

NGS pipeline in UGENE

Overview of NGS Pipelines in UGENE UGENE is a free bioinformatics platform that integrates dozens of well-known biological tools and algorithms and provides both graphical and command line interfaces for them. It is designed to solve various complex computational tasks in bioinformatics. One of the areas is analysis of sequencing data produced by popular modern more…



January 15th, 2015 : Alignment of Short Reads

Short Reads Mapping

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…