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ugene

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)