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
computational 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
* 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
UGENE has modular structure and almost all its functionality comes
within plugins. Internally UGENE is designed with support of
parallelism to make profit from using multicore computers. Every
computational 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
options and the program version, then exit.
--test-timeout=<number-of-seconds>
set timeout for tests execution in seconds
--test-threads=<number-of-threads>
set number of threads in test runner that can run at the same
time
--test-suite=<path-to-test-suite> [suite2 ...]
load test suites and run them
--test-report=<test-report-dir>
set directory where test report will be placed
--task=<path-to-schema or schema-name> [schema-options]
run given workflow schema
--status-bar-hide
don't show task status bar
--settings-load-file=<path-to-settings-file>
load custom UGENE settings file
--log-teamcity-out
output test's messages for TeamCity system
--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
--local-task-run=<local-task-to-run>
read files with serialized UGENE tasks and run them
--local-task-info
create machine info file
--congene-stay-alive
COMMANDS
UGENE has commands for most significant features. Commands can be run
as
ugene <command-name> [command-arguments]
ugene --task=<command-name> [command-arguments]
align aligns input msa using MUSCLE3 tool and writes output in
CLUSTALW format
--in=<path-to-file> path to input msa file
--out=<path-to-file> path to output file
Example: ugene align --in=14-3-3.sto --out=14-3-3_aligned.aln
convert-seq
converts sequences between formats
--in=<path-to-file> path to input sequence file
--format=<format-name> format name of output file. Currently,
following formats are supported:
fasta
genbank
raw
--out=<path-to-file> path to output file
Example: ugene convert-seq --in=human_T1.fa --format=genbank
--out=human_T1.gbk
convert-msa
converts multiple sequence alignment between formats
--in=<path-to-file> path to input msa file
--format=<format-name> format name of output file. Currently,
following formats are supported:
clustal
stockholm
msf
srfasta
--out=<path-to-file> path to output file
Example: ugene convert-msa --in=CBS.sto --format=clustal
--out=CBS.aln
find-orfs
finds Open Reading Frames in supplied sequence and writes
results as annotations
--in=<path-to-file> path to input sequence file
--name=<name-of-annotations> name of annotated regions (default:
"ORF")
--min-length=<number> ignore ORFs shorter than this number
(default: 100)
--require-stop-codon=<boolean-value> ignore boundary ORFs which
last beyound the search region i.e. have no stop codon within
the range (default: false)
true
false
--require-init-codon=<boolean-value> allow or not ORFs starting
with any codon other than terminator(default: true)
true
false
--allow-alternative-codons=<boolean-value> allow ORFs starting
with alternative initiation codons, accordingly to the current
translation table(default: false)
true
false
--out=<path-to-file> path to output file with annotations
Example: ugene find-orfs --in=human_T1.fa --out=human_orfs.gbk
--require-init-codon=false
find-repeats
find repeats in supplied sequence and writes results as
annotations
--in=<path-to-file> path to input sequence file
--name=<name-of-annotations> name of annotated regions (default:
"repeat_unit")
--min-length=<number> minimum length of repeats (default:5)
--identity=<number> repeats identity in percents (default:100)
--min-distance=<number> minimum distance between repeats
(default:0)
--max-distance=<number> maximum distance between repeats
(default: 5000)
--inverted=<boolean-value> search for inverted repeats (default:
false)
true
false
--out=<path-to-file> path to output file with annotations
Example: ugene find-repeats --in=murine.gb --out=out.gb
--identity=99
find-sw
find given pattern in supplied sequence and writes results as
annotations
--in=<path-to-file> path to input sequence file
--name=<name-of-annotations> name of annotated regions (default:
"misc_feature")
--ptrn=<sequence> a subsequence pattern to look for (e.g AGGCCT)
--score=<number> similarity with pattern in percents (default:
90)
--matrix=<matrix-name> the scoring matrix (default: Auto)
Auto
blosum62
dna
rna
dayhoff
gonnet
pam250
--filter=<filter-name> result filtering strategy (default:
filter-intersections)
filter-intersections
none
--out=<path-to-file> path to output file with annotations
Example: ugene find-sw --in=human_T1.fa --out=human_T1_sw.gbk
--ptrn=TGCT --filter=none
hmm2-build
builds and(or) calibrates HMM profile using HMMER2 tools
--in=<path-to-file> path to input msa file
--name=<name-of-hmm> descriptive name of the HMM profile
(default: empty)
--calibrate=<boolean-value> enables/disables profile calibration
(default: true)
true
false
--seed=<number> the random seed, a positive integer (default: 0)
--out=<path-to-file> path to output file with HMM profile
Example: ugene hmm2-build --in=CBS.sto --out=CBS.hmm
--calibrate=true
hmm2-search
searches input sequence for significantly similar sequence
matches to given profile HMM using HMMER2 tools
--seq=<path-to-file> input sequence to search in
--hmm=<path-to-file> input HMM profile to search for
--name=<name-of-annotations> name of the result annotations
(default: "hmm_signal")
--e-val=<number> filter by high e-value. Positive integer value.
Filtering is done by 1e-<number> (default: 1)
--score=<float-value> filter by low score(default: -1000000000)
--out=<path-to-file> path to output file with annotations
Example: ugene hmm2-search --seq=CBS_seq.fa --hmm=CBS.hmm
--out=CBS_out.gbk --e-val=2
remote-request
--in=<path-to-file> input file with sequence(s)
--out=<path-to-file> output file with annotations in Genbank
format
--db=<name-of-db> name of database to search in
ncbi-blastn for nucleotide sequence
ncbi-cdd for amino
ncbi-blastp for amino
--eval=<number> statistical significance threshold for reporting
matches against database sequences(default: 10). Values can be
one of:
1
10
100
1000
1e-10
1e-100
--hits=<number>
maximum number of hits, that will be shown. Positive integer
(default: 10)
--name=<name-of-annotations> name of result annotations
(default: "cdd_result" or "blast_result")
--short=<boolean-value> determines wether or not to optimize
search for short sequences (default: false)
true
false
--blast-output=<path-to-file>
path to file with NCBI-BLAST output. Works only for databases
ncbi-blastp and ncbi-blastn.
Example: ugene remote-request --in=seq.fa --db=ncbi-blastp
--hits=100 --blast-output=blast.xml --out=res.gb
BUGS
If you find a bug, please report it at ugene@unipro.ru.
AUTHOR
ugene was created by Unipro (http://unipro.ru)
24 May 2010