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UGENE(1) General Commands Manual UGENE(1) NAME UGENE - integrated bioinformatics suite SYNOPSIS ugene -ui ugene [OPTIONS] DESCRIPTION UGENE is a cross-platform environment for DNA and protein sequence analysis. UGENE integrates the most popular bioinformatics computa- tional algorithms and provides both GUI and command line interface for performing complex analysis of the genomic data. The main features of UGENE: * View and analysis of annotated DNA or protein sequences * Chromatograms visualization and editing * Integrated 3D viewer for files in PDB and MMDB formats * Integrated support of search requests to NCBI databases * Multiple sequence alignment using MUSCLE3, MUSCLE4 and KAlign * HMM profiles build and search, based on the source of HMMER2 and HMMER3 * Modern protein secondary structure prediction algorithms based on GORIV and PsiPred * Phylogenetic analysis with Phylip * PCR Primers design using Primer3 package * Cloning in silico * Search for transcription factor binding sites in DNA sequences using SITECON * Search for restriction enzymes and integration with REBASE * Search for direct and invert repeats * DNA reference assembly using Bowtie * Protein back translation * Search for ORFs * Designer for complex computational workflows and queries UGENE has modular structure and almost all its functionality comes within plugins. Internally UGENE is designed with support of paral- lelism to make profit from using multicore computers. Every computa- tional task in UGENE is performed in background and does not block user interaction with graphical interface. OPTIONS -ui run GUI version of UGENE --help print a usage message briefly summarizing all command-line op- tions and the program version, then exit. --license dump license information --task=<path-to-schema or schema-name> [schema-options] run given workflow schema --status-bar-hide don't show task status bar --ini-file=<path-to-settings-file> load custom UGENE settings file --log-no-show-level don't show message level at log --log-no-show-date don't show date&time info at log --log-no-show-category don't show message category at log --log-level-trace show trace log messages --log-level-none don't show log messages --log-level-info show error and info log messages (default) --log-level-error show only error log messages --log-level-details show details log messages --log-color-output colored output messages --task-remote-machine=<path-to-machine-file> run provided tasks on given remote machine --ugene-stay-alive do not stop ugene after finishing given tasks --transl=<language-code> load translations of specified language. Language is specified as a two-letter ISO 639 language code COMMANDS UGENE has commands for most significant features. Commands can be run as ugene <command-name> [command-arguments] ugene --task=<command-name> [command-arguments] See help for each command running ugene --help=<command-name>. List of available commands can be dumped using ugene --help. BUGS If you find a bug, please report it at ugene@unipro.ru. AUTHOR ugene was created by Unipro (http://unipro.ru) 11 February 2011 UGENE(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | COMMANDS | BUGS | AUTHOR
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