UGENE

Key features

The software supports the following features:

Create, edit, and annotate nucleic acid and protein sequences

Fast search in a sequence

Multiple sequence alignment: Clustal W and O, MUSCLE, Kalign, MAFFT, T-Coffee

Create and use shared storage, e.g., lab database

Search through online databases: National Center for Biotechnology Information (NCBI), Protein Data Bank (PDB), UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, DAS servers

Local and NCBI Genbank BLAST search

Open reading frame finder

Restriction enzyme finder with integrated REBASE restriction enzymes list

Integrated Primer3 package for PCR primer design

Plasmid construction and annotation

Cloning in silico by designing of cloning vectors

Genome mapping of short reads with Bowtie, BWA, and UGENE Genome Aligner

Visualize next generation sequencing data (BAM files) using UGENE Assembly Browser

Variant calling with SAMtools

RNA-Seq data analysis with Tuxedo pipeline (TopHat, Cufflinks, etc.)

ChIP-seq data analysis with Cistrome pipeline (MACS, CEAS, etc.)

Raw NGS data processing

HMMER 2 and 3 packages integration

Chromatogram viewer

Search for transcription factor binding sites (TFBS) with weight matrix and SITECON algorithms

Search for direct, inverted, and tandem repeats in DNA sequences

Local sequence alignment with optimized Smith-Waterman algorithm

Build (using integrated PHYLIP neighbor joining, MrBayes, or PhyML Maximum Likelihood) and edit phylogenetic trees

Combine various algorithms into custom workflows with UGENE Workflow Designer

Contigs assembly with CAP3

3D structure viewer for files in Protein Data Bank (PDB) and Molecular Modeling Database (MMDB) formats, anaglyph view support

Predict protein secondary structure with GOR IV and PSIPRED algorithms

Construct dot plots for nucleic acid sequences

mRNA alignment with Spidey

Search for complex signals with ExpertDiscovery

Search for a pattern of various algorithms' results in a nucleic acid sequence with UGENE Query Designer

PCR in silico for primer designing and mapping

Spade de novo assembler

Sequence View

The Sequence View is used to visualize, analyze and modify nucleic acid or protein sequences. Depending on the sequence type and the options selected, the following views can be present in the Sequence View window:

3D structure view

Circular view

Chromatogram view

Graphs View: GC-content, AG-content, and other

Dot plot view

Alignment Editor

The Alignment Editor allows working with multiple nucleic acid or protein sequences - aligning them, editing the alignment, analyzing it, storing the consensus sequence, building a phylogenetic tree, and so on.

Phylogenetic Tree Viewer

The Phylogenetic Tree Viewer helps to visualize and edit phylogenetic trees. It is possible to synchronize a tree with the corresponding multiple alignment used to build the tree.

Assembly Browser

The Assembly Browser project was started in 2010 as an entry for Illumina iDEA Challenge 2011. The browser allows users to visualize and browse large (up to hundreds of millions of short reads) next generation sequence assemblies. It supports SAM, BAM (the binary version of SAM), and ACE formats. Before browsing assembly data in UGENE, an input file is converted to a UGENE database file automatically. This approach has its pros and cons. The pros are that this allows viewing the whole assembly, navigating in it, and going to well-covered regions rapidly. The cons are that a conversion may take time for a large file, and needs enough disk space to store the database.

Workflow Designer

UGENE Workflow Designer allows creating and running complex computational workflow schemas.

The distinguishing feature of Workflow Designer, relative to other bioinformatics workflow management systems is that workflows are executed on a local computer. It helps to avoid data transfer issues, whereas other tools’ reliance on remote file storage and internet connectivity does not.

The elements that a workflow consists of correspond to the bulk of algorithms integrated into UGENE. Using Workflow Designer also allows creating custom workflow elements. The elements can be based on a command-line tool or a script.

Workflows are stored in a special text format. This allows their reuse, and transfer between users.

A workflow can be run using the graphical interface or launched from the command line. The graphical interface also allows controlling the workflow execution, storing the parameters, and so on.

There is an embedded library of workflow samples to convert, filter, and annotate data, with several pipelines to analyze NGS data developed in collaboration with NIH NIAID. A wizard is available for each workflow sample.

Supported biological data formats

Sequences and annotations: FASTA (.fa), GenBank (.gb), EMBL (.emb), GFF (.gff)

Multiple sequence alignments: Clustal (.aln), MSF (.msf), Stockholm (.sto), Nexus (.nex)

3D structures: PDB (.pdb), MMDB (.prt)

Chromatograms: ABIF (.abi), SCF (.scf)

Short reads: Sequence Alignment/Map(SAM) (.sam), binary version of SAM (.bam), ACE (.ace), FASTQ (.fastq)

Phylogenetic trees: Newick (.nwk), PHYLIP (.phy)

Other formats: Bairoch (enzymes info), HMM (HMMER profiles), PWM and PFM (position matrices), SNP and VCF4 (genome variations)

Release cycle

UGENE is primarily developed by Unipro LLC with headquarters in Akademgorodok of Novosibirsk, Russia. Each iteration lasts about 1–2 months, followed by a new release. Development snapshots may also be downloaded.

The features to include in each release are mostly initiated by users.

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