UGENE is a free software aimed to integrate most of the important molecular biology tools within a single graphical environment. UGENE runs on Linux, Windows and MacOS platforms and is able to utilize resources of modern multi-core and GPU hardware.
Features: * Visual representation of annotated DNA or protein sequences * Chromatograms visualization * Search for ORFs * Integrated support of search requests to NCBI databases * Multiple sequence alignment with port of MUSCLE3,4 and KAlign * Easy-to-use search with HMM profiles using adopted HMMER2 package * Integarion of the newest methods for HMM profile search based on HMMER3 * Integrated 3D viewer for files in PDB and MMDB formats * Phylogenetic analysis with Phylip, integrated tree viewer; * Modern protein secondary structure prediction algorigthms based on GORIV and PsiPred * Integration of PRIMER3 package * Designer for custom computational workflows * Search for transcription factor binding sites (TFBS) in DNA sequences * Restriction enzymes search and integration with REBASE restrictions enzymes database * Search for direct and inverted repeats in DNA sequences * Complete Smith-Waterman algorithm implementation
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