Tutorials: How to Save View States with Bookmarks in UGENE In UGENE you can save and restore object views states using the bookmark mechanism An Object view is a graphical representation for structured biological data, or Object, in UGENE. A single object view can visualize one or several objects of different types. PDB File Example more…

Tutorial: UGENE as a Transcription Factor Binding Site Prediction Tool Today's topic is SITECON plugin, which is a transcription factor binding site prediction tool. The tool is developed in Institute of Cytology and Genetics SB RAS. SITECON Description The basis of the search is a set of conservative (conformational and physicochemical) properties of transcription factor more…

Tutorial: HMMER3 in UGENE Today we will use a powerful tool for searching sequence databases for homologs of protein sequence and for making a protein alignment, HMMER 3, with UGENE. The UGENE version of HMMER is aimed to provide a wider user audience with a high-performance HMMER-compatible solution. The plugin with GUI, as well as more…

Tutorial: UGENE as a Transcription Factor Binding Site Prediction Tool today's topic is the Weight Matrix plugin, a part of UGENE. It allows to perform the transcription factor binding site search. User can create and save position weight and frequency matrices and align them to an opened sequence. To invoke the plugin, we open a more…

Tutorial: Performing profile-to-profile and profile-to-sequence MUSCLE alignments Our users can use powerful MUSCLE alignment tool in order to create Multiple Sequence Alignment. But it is also possible to align two existing alignments in UGENE, which is also called „profile-profile alignment“. The operation could be useful for alignments of related sequences and will only insert gap columns more…

Tutorial: Search for Sequence Repeats with UGENE Today we will search for repeats in a DNA sequence in UGENE. This is one of the types of biological sequence analysis that UGENE ca do. To do so, we open such a sequence, for example of the FASTA format. Now we activate the sequence view context menu more…

Tutorial: Chromatogram Analysis in UGENE Here we discuss the hottest topics introduced by our users and show the helpful ways of using UGENE, a free cross-platform genome analysis suite. UGENE makes it possible to do chromatogram analysis and work with chromatogram files such as ABI files and SCF format files. To watch a chromatogram, we more…

Tutorial: Opening Reading Frame Finder in UGENE Here we discuss the hottest topics introduced by our users and show the helpful ways of using UGENE, a free cross-platform genome analysis suite. Today we will continue working with sequence analysis in UGENE and consider searching for open reading frames in a DNA sequence introducing UGENE as more…

Tutorial: Create a Multiple Sequence Alignment Here we discuss the hottest topics introduced by our users and show the helpful ways of using UGENE, a free cross-platform genome analysis suite. Earlier we've been using UGENE MUSCLE multiple alignment tool plugin to create a multiple sequence alignment. We were using a limited number of sequences to more…

Tutorial: How to Search for Restriction Enzymes Here we discuss the hottest topics introduced by our users and show the helpful ways of using UGENE, a free cross-platform genome analysis suite. Search for Restriction Enzymes With UGENE restriction site finder you can search for restriction enzymes cut sites in a DNA sequence. Today we will more…