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UGENE is free open-source bioinformatics software.〔〔 It works on a desktop computer with Windows, Mac OS X or Linux. UGENE helps biologists to analyze various biological data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. The data can be stored both locally (on a personal computer) and on a shared storage (e.g. a lab database). UGENE integrates dozens of well-known biological tools and algorithms, as well as original tools in context of genomics, evolutionary biology, virology and other branches of life science. UGENE provides a graphical interface for the pre-built tools so biologists without programming skills can access those tools more easily. Using UGENE Workflow Designer, it is possible to streamline a multi-step analysis. The workflow consists of blocks such as data readers, blocks executing embedded tools/algorithms and data writers. Blocks can be created with command line tools or a script. A set of sample workflows is available in the Workflow Designer (for annotating sequences, conversion of data formats, NGS data analysis, etc.) Besides the graphical interface, UGENE also provides a command-line interface. A workflow made by the Workflow Designer can be executed using the command-line interface. In order to provide better performance, UGENE utilizes multicore CPUs and GPUs to optimize a few algorithms.〔〔 == Key features == The software supports the following features: * Creating, editing and annotating nucleic acid and protein sequences * Fast search in a sequence * Multiple sequence alignment: ClustalW, ClustalO, MUSCLE, Kalign, MAFFT, T-Coffee * Creating and using a shared storage (e.g.lab database) * Search through online databases: NCBI, 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 * Visualization of 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 * HMMER2 and HMMER3 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 * Building (using integrated PHYLIP Neighbor Joining, (MrBayes ) or (PhyML ) Maximum Likelihood) and editing phylogenetic trees * Combining various algorithms into custom workflows with UGENE Workflow Designer * Contigs assembly with (CAP3 ) * 3D structure viewer for files in PDB and MMDB formats, anaglyph view support * Protein secondary structure prediction with GOR IV and PSIPRED algorithms * Constructing dotplots 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 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「UGENE」の詳細全文を読む スポンサード リンク
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