Tutorial: Metagenomic Classification with Kraken In this tutorial we will learn how to classify our metagenomic reads obtained with Illumina sequencing platform with Kraken, a system for assigning taxonomic labels to short DNA sequences. You can find more information about Kraken here: Kraken website: https://ccb.jhu.edu/software/kraken/ Kraken manual: http://ccb.jhu.edu/software/kraken/MANUAL.html We have collected field mosquitoes from different more…
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…
Multiple Sequence Alignment Overview
Tutorial: UGENE Multiple Alignment Overview Multiple Alignment Editor has many features common to multiple sequence alignment tools like highlighting of differences 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…
Public Databases
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…
UGENE 1.16
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…
Shared Databases 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…
Amino-translations and Identical Sequences
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…
SNP Search and SNP Effect
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…
Pairwise Alignment and Remove Gaps
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…
NGS Pipelines 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…