exonerate -h 與--help 幫助文檔

exonerate -h

** (process:121002): WARNING **: 21:41:53.839: Compiled with assertion checking - will run slowly

exonerate from exonerate version 2.4.0

Using glib version 2.42.2

Built on Mar 24 2016

exonerate: A generic sequence comparison tool

Guy St.C. Slater. guy@ebi.ac.uk. 2000-2009.

Examples of use:

1. Ungapped alignment of any DNA or protein sequences:

? ? exonerate queries.fa targets.fa

2. Gapped alignment of Mouse proteins to Fugu proteins:

? ? exonerate --model affine:local mouse.fa fugu.fa

3. Find top 10 matches of each EST to a genome:

? ? exonerate --model est2genome --bestn 10 est.fa genome.fa

4. Find proteins with at least a 50% match to a genome:

? ? exonerate --model protein2genome --percent 50 p.fa g.fa

5. Perform a full Smith-Waterman-Gotoh alignment:

? ? exonerate --model affine:local --exhaustive yes a.fa b.fa

6. Many more combinations are possible.? To find out more:

? ? exonerate --help

? ? man exonerate

General Options:

---------------

-h --shorthelp [FALSE] <TRUE>

? --help [FALSE]

-v --version [FALSE]

Sequence Input Options:

----------------------

-q --query [mandatory]? <*** empty list ***>

-t --target [mandatory]? <*** empty list ***>

-Q --querytype [unknown]

-T --targettype [unknown]

? --querychunkid [0]

? --targetchunkid [0]

? --querychunktotal [0]

? --targetchunktotal [0]

-V --verbose [1]

Translation Options:

-------------------

? --geneticcode [1]

Analysis Options:

----------------

-E --exhaustive [FALSE]

-B --bigseq [FALSE]

-r --revcomp [TRUE]

? --forcescan [none]

? --saturatethreshold [0]

? --customserver [NULL]

-c --cores [1]

Fasta Database Options:

----------------------

? --fastasuffix [.fa]

Gapped Alignment Options:

------------------------

-m --model [ungapped]

-s --score [100]

? --percent [0.0]

? --showalignment [TRUE]

? --showsugar [FALSE]

? --showcigar [FALSE]

? --showvulgar [TRUE]

? --showquerygff [FALSE]

? --showtargetgff [FALSE]

? --ryo [NULL]

-n --bestn [0]

-S --subopt [TRUE]

-g --gappedextension [TRUE]

? --refine [none]

? --refineboundary [32]

Viterbi algorithm options:

-------------------------

-D --dpmemory [32]

Code generation options:

-----------------------

-C --compiled [TRUE]

Heuristic Options:

-----------------

? --terminalrangeint [12]

? --terminalrangeext [12]

? --joinrangeint [12]

? --joinrangeext [12]

? --spanrangeint [12]

? --spanrangeext [12]

Seeded Dynamic Programming options:

----------------------------------

-x --extensionthreshold [50]

? --singlepass [TRUE]

BSDP algorithm options:

----------------------

? --joinfilter [0]

Sequence Options:

----------------

-A --annotation [none]

Symbol Comparison Options:

-------------------------

? --softmaskquery [FALSE]

? --softmasktarget [FALSE]

-d --dnasubmat [nucleic]

-p --proteinsubmat [blosum62]

Alignment Seeding Options:

-------------------------

-M --fsmmemory [256]

? --forcefsm [none]

? --wordjump [1]

? --wordambiguity [1]

Affine Model Options:

--------------------

-o --gapopen [-12]

-e --gapextend [-4]

? --codongapopen [-18]

? --codongapextend [-8]

NER Model Options:

-----------------

? --minner [10]

? --maxner [50000]

? --neropen [-20]

Intron Modelling Options:

------------------------

? --minintron [30]

? --maxintron [200000]

-i --intronpenalty [-30]

Frameshift Options:

------------------

-f --frameshift [-28]

Alphabet Options:

----------------

? --useaatla [TRUE]

HSP creation options:

--------------------

? --hspfilter [0]

? --useworddropoff [TRUE]

? --seedrepeat [1]

? --dnawordlen [12]

? --proteinwordlen [6]

? --codonwordlen [12]

? --dnahspdropoff [30]

? --proteinhspdropoff [20]

? --codonhspdropoff [40]

? --dnahspthreshold [75]

? --proteinhspthreshold [30]

? --codonhspthreshold [50]

? --dnawordlimit [0]

? --proteinwordlimit [4]

? --codonwordlimit [4]

? --geneseed [0]

? --geneseedrepeat [3]

Alignment options:

-----------------

? --alignmentwidth [80]

? --forwardcoordinates [TRUE]

SAR Options:

-----------

? --quality [0]

Splice Site Prediction Options:

------------------------------

? --splice3 [primate]

? --splice5 [primate]

? --forcegtag [FALSE]

--




exonerate --help

** (process:121224): WARNING **: 21:45:39.272: Compiled with assertion checking - will run slowly

exonerate from exonerate version 2.4.0

Using glib version 2.42.2

Built on Mar 24 2016

exonerate: A generic sequence comparison tool

Guy St.C. Slater. guy@ebi.ac.uk. 2000-2009.

Examples of use:

1. Ungapped alignment of any DNA or protein sequences:

? ? exonerate queries.fa targets.fa

2. Gapped alignment of Mouse proteins to Fugu proteins:

? ? exonerate --model affine:local mouse.fa fugu.fa

3. Find top 10 matches of each EST to a genome:

? ? exonerate --model est2genome --bestn 10 est.fa genome.fa

4. Find proteins with at least a 50% match to a genome:

? ? exonerate --model protein2genome --percent 50 p.fa g.fa

5. Perform a full Smith-Waterman-Gotoh alignment:

? ? exonerate --model affine:local --exhaustive yes a.fa b.fa

6. Many more combinations are possible.? To find out more:

? ? exonerate --help

? ? man exonerate

General Options:

---------------

-h --shorthelp

Display compact help text

Environment variable: $EXONERATE_EXONERATE_SHORTHELP (Not set)

Default: "FALSE"

--help

Displays verbose help text

Environment variable: $EXONERATE_EXONERATE_HELP (Not set)

Default: "FALSE"

Using: <TRUE>

-v --version

Show version number for this program

Environment variable: $EXONERATE_EXONERATE_VERSION (Not set)

Default: "FALSE"

Sequence Input Options:

----------------------

-q --query <path>

Specify query sequences as a fasta format file

Environment variable: $EXONERATE_EXONERATE_QUERY (Not set)

*** This argument is mandatory ***

<*** empty list ***>

-t --target <path>

Specify target sequences as a fasta format file

Environment variable: $EXONERATE_EXONERATE_TARGET (Not set)

*** This argument is mandatory ***

<*** empty list ***>

-Q --querytype <alphabet type>

Specify query alphabet type

Environment variable: $EXONERATE_EXONERATE_QUERYTYPE (Not set)

Default: "unknown"

-T --targettype <alphabet type>

Specify target alphabet type

Environment variable: $EXONERATE_EXONERATE_TARGETTYPE (Not set)

Default: "unknown"

--querychunkid

Specify query job number

Environment variable: $EXONERATE_EXONERATE_QUERYCHUNKID (Not set)

Default: "0"

--targetchunkid

Specify target job number

Environment variable: $EXONERATE_EXONERATE_TARGETCHUNKID (Not set)

Default: "0"

--querychunktotal

Specify total number of query jobs

Environment variable: $EXONERATE_EXONERATE_QUERYCHUNKTOTAL (Not set)

Default: "0"

--targetchunktotal

Specify total number of target jobs

Environment variable: $EXONERATE_EXONERATE_TARGETCHUNKTOTAL (Not set)

Default: "0"

-V --verbose <level>

Show search progress

Environment variable: $EXONERATE_EXONERATE_VERBOSE (Not set)

Default: "1"

Translation Options:

-------------------

--geneticcode

Use built-in or custom genetic code

Environment variable: $EXONERATE_EXONERATE_GENETICCODE (Not set)

Default: "1"

Analysis Options:

----------------

-E --exhaustive

Perform exhaustive alignment (slow)

Environment variable: $EXONERATE_EXONERATE_EXHAUSTIVE (Not set)

Default: "FALSE"

-B --bigseq

Allow rapid comparison between big sequences

Environment variable: $EXONERATE_EXONERATE_BIGSEQ (Not set)

Default: "FALSE"

-r --revcomp

Also search reverse complement of query and target

Environment variable: $EXONERATE_EXONERATE_REVCOMP (Not set)

Default: "TRUE"

--forcescan <[q|t]>

Force FSM scan on query or target sequences

Environment variable: $EXONERATE_EXONERATE_FORCESCAN (Not set)

Default: "none"

--saturatethreshold <int>

Word saturation threshold

Environment variable: $EXONERATE_EXONERATE_SATURATETHRESHOLD (Not set)

Default: "0"

--customserver <command>

Custom command to send non-standard server

Environment variable: $EXONERATE_EXONERATE_CUSTOMSERVER (Not set)

Default: "NULL"

-c --cores <number>

Number of cores/CPUs/threads for alignment computation

Environment variable: $EXONERATE_EXONERATE_CORES (Not set)

Default: "1"

Fasta Database Options:

----------------------

--fastasuffix <suffix>

Fasta file suffix filter (in subdirectories)

Environment variable: $EXONERATE_EXONERATE_FASTASUFFIX (Not set)

Default: ".fa"

Gapped Alignment Options:

------------------------

-m --model <alignment model>

Specify alignment model type

Supported types:

? ? ungapped ungapped:trans

? ? affine:global affine:bestfit affine:local affine:overlap

? ? est2genome ner protein2dna protein2genome

? ? protein2dna:bestfit protein2genome:bestfit

? ? coding2coding coding2genome cdna2genome genome2genome

Environment variable: $EXONERATE_EXONERATE_MODEL (Not set)

Default: "ungapped"

-s --score <threshold>

Score threshold for gapped alignment

Environment variable: $EXONERATE_EXONERATE_SCORE (Not set)

Default: "100"

--percent <threshold>

Percent self-score threshold

Environment variable: $EXONERATE_EXONERATE_PERCENT (Not set)

Default: "0.0"

--showalignment

Include (human readable) alignment in results

Environment variable: $EXONERATE_EXONERATE_SHOWALIGNMENT (Not set)

Default: "TRUE"

--showsugar

Include 'sugar' format output in results

Environment variable: $EXONERATE_EXONERATE_SHOWSUGAR (Not set)

Default: "FALSE"

--showcigar

Include 'cigar' format output in results

Environment variable: $EXONERATE_EXONERATE_SHOWCIGAR (Not set)

Default: "FALSE"

--showvulgar

Include 'vulgar' format output in results

Environment variable: $EXONERATE_EXONERATE_SHOWVULGAR (Not set)

Default: "TRUE"

--showquerygff

Include GFF output on query in results

Environment variable: $EXONERATE_EXONERATE_SHOWQUERYGFF (Not set)

Default: "FALSE"

--showtargetgff

Include GFF output on target in results

Environment variable: $EXONERATE_EXONERATE_SHOWTARGETGFF (Not set)

Default: "FALSE"

--ryo <format>

Roll-your-own printf-esque output format

Environment variable: $EXONERATE_EXONERATE_RYO (Not set)

Default: "NULL"

-n --bestn <number>

Report best N results per query

Environment variable: $EXONERATE_EXONERATE_BESTN (Not set)

Default: "0"

-S --subopt

Search for suboptimal alignments

Environment variable: $EXONERATE_EXONERATE_SUBOPT (Not set)

Default: "TRUE"

-g --gappedextension

Use gapped extension (default is SDP)

Environment variable: $EXONERATE_EXONERATE_GAPPEDEXTENSION (Not set)

Default: "TRUE"

--refine

Alignment refinement strategy [none|full|region]

Environment variable: $EXONERATE_EXONERATE_REFINE (Not set)

Default: "none"

--refineboundary

Refinement region boundary

Environment variable: $EXONERATE_EXONERATE_REFINEBOUNDARY (Not set)

Default: "32"

Viterbi algorithm options:

-------------------------

-D --dpmemory <Mb>

Maximum memory to use for DP tracebacks (Mb)

Environment variable: $EXONERATE_EXONERATE_DPMEMORY (Not set)

Default: "32"

Code generation options:

-----------------------

-C --compiled

Use compiled viterbi implementations

Environment variable: $EXONERATE_EXONERATE_COMPILED (Not set)

Default: "TRUE"

Heuristic Options:

-----------------

--terminalrangeint

Internal terminal range

Environment variable: $EXONERATE_EXONERATE_TERMINALRANGEINT (Not set)

Default: "12"

--terminalrangeext

External terminal range

Environment variable: $EXONERATE_EXONERATE_TERMINALRANGEEXT (Not set)

Default: "12"

--joinrangeint

Internal join range

Environment variable: $EXONERATE_EXONERATE_JOINRANGEINT (Not set)

Default: "12"

--joinrangeext

External join range

Environment variable: $EXONERATE_EXONERATE_JOINRANGEEXT (Not set)

Default: "12"

--spanrangeint

Internal span range

Environment variable: $EXONERATE_EXONERATE_SPANRANGEINT (Not set)

Default: "12"

--spanrangeext

External span range

Environment variable: $EXONERATE_EXONERATE_SPANRANGEEXT (Not set)

Default: "12"

Seeded Dynamic Programming options:

----------------------------------

-x --extensionthreshold

Gapped extension threshold

Environment variable: $EXONERATE_EXONERATE_EXTENSIONTHRESHOLD (Not set)

Default: "50"

--singlepass

Generate suboptimal alignment in a single pass

Environment variable: $EXONERATE_EXONERATE_SINGLEPASS (Not set)

Default: "TRUE"

BSDP algorithm options:

----------------------

--joinfilter

BSDP join filter threshold

Environment variable: $EXONERATE_EXONERATE_JOINFILTER (Not set)

Default: "0"

Sequence Options:

----------------

-A --annotation <path>

Path to sequence annotation file

Environment variable: $EXONERATE_EXONERATE_ANNOTATION (Not set)

Default: "none"

Symbol Comparison Options:

-------------------------

--softmaskquery

Allow softmasking on the query sequence

Environment variable: $EXONERATE_EXONERATE_SOFTMASKQUERY (Not set)

Default: "FALSE"

--softmasktarget

Allow softmasking on the target sequence

Environment variable: $EXONERATE_EXONERATE_SOFTMASKTARGET (Not set)

Default: "FALSE"

-d --dnasubmat <name>

DNA substitution matrix

Environment variable: $EXONERATE_EXONERATE_DNASUBMAT (Not set)

Default: "nucleic"

-p --proteinsubmat <name>

Protein substitution matrix

Environment variable: $EXONERATE_EXONERATE_PROTEINSUBMAT (Not set)

Default: "blosum62"

Alignment Seeding Options:

-------------------------

-M --fsmmemory <Mb>

Memory limit for FSM scanning

Environment variable: $EXONERATE_EXONERATE_FSMMEMORY (Not set)

Default: "256"

--forcefsm <fsm type>

Force FSM type ( normal | compact )

Environment variable: $EXONERATE_EXONERATE_FORCEFSM (Not set)

Default: "none"

--wordjump

Jump between query words

Environment variable: $EXONERATE_EXONERATE_WORDJUMP (Not set)

Default: "1"

--wordambiguity

Number of ambiguous words to expand

Environment variable: $EXONERATE_EXONERATE_WORDAMBIGUITY (Not set)

Default: "1"

Affine Model Options:

--------------------

-o --gapopen <penalty>

Affine gap open penalty

Environment variable: $EXONERATE_EXONERATE_GAPOPEN (Not set)

Default: "-12"

-e --gapextend <penalty>

Affine gap extend penalty

Environment variable: $EXONERATE_EXONERATE_GAPEXTEND (Not set)

Default: "-4"

--codongapopen <penalty>

Codon affine gap open penalty

Environment variable: $EXONERATE_EXONERATE_CODONGAPOPEN (Not set)

Default: "-18"

--codongapextend <penalty>

Codon affine gap extend penalty

Environment variable: $EXONERATE_EXONERATE_CODONGAPEXTEND (Not set)

Default: "-8"

NER Model Options:

-----------------

--minner <length>

Minimum NER length

Environment variable: $EXONERATE_EXONERATE_MINNER (Not set)

Default: "10"

--maxner <length>

Maximum NER length

Environment variable: $EXONERATE_EXONERATE_MAXNER (Not set)

Default: "50000"

--neropen <score>

NER open penalty

Environment variable: $EXONERATE_EXONERATE_NEROPEN (Not set)

Default: "-20"

Intron Modelling Options:

------------------------

--minintron <length>

Minimum intron length

Environment variable: $EXONERATE_EXONERATE_MININTRON (Not set)

Default: "30"

--maxintron <length>

Maximum intron length

Environment variable: $EXONERATE_EXONERATE_MAXINTRON (Not set)

Default: "200000"

-i --intronpenalty <score>

Intron Opening penalty

Environment variable: $EXONERATE_EXONERATE_INTRONPENALTY (Not set)

Default: "-30"

Frameshift Options:

------------------

-f --frameshift <penalty>

Frameshift creation penalty

Environment variable: $EXONERATE_EXONERATE_FRAMESHIFT (Not set)

Default: "-28"

Alphabet Options:

----------------

--useaatla

Use three-letter abbreviation for AA names

Environment variable: $EXONERATE_EXONERATE_USEAATLA (Not set)

Default: "TRUE"

HSP creation options:

--------------------

--hspfilter

Aggressive HSP filtering level

Environment variable: $EXONERATE_EXONERATE_HSPFILTER (Not set)

Default: "0"

--useworddropoff

Use word neighbourhood dropoff

Environment variable: $EXONERATE_EXONERATE_USEWORDDROPOFF (Not set)

Default: "TRUE"

--seedrepeat

Seeds per diagonal required for HSP seeding

Environment variable: $EXONERATE_EXONERATE_SEEDREPEAT (Not set)

Default: "1"

--dnawordlen <bp>

Wordlength for DNA words

Environment variable: $EXONERATE_EXONERATE_DNAWORDLEN (Not set)

Default: "12"

--proteinwordlen <aa>

Wordlength for protein words

Environment variable: $EXONERATE_EXONERATE_PROTEINWORDLEN (Not set)

Default: "6"

--codonwordlen <bp>

Wordlength for codon words

Environment variable: $EXONERATE_EXONERATE_CODONWORDLEN (Not set)

Default: "12"

--dnahspdropoff <score>

DNA HSP dropoff score

Environment variable: $EXONERATE_EXONERATE_DNAHSPDROPOFF (Not set)

Default: "30"

--proteinhspdropoff <score>

Protein HSP dropoff score

Environment variable: $EXONERATE_EXONERATE_PROTEINHSPDROPOFF (Not set)

Default: "20"

--codonhspdropoff <score>

Codon HSP dropoff score

Environment variable: $EXONERATE_EXONERATE_CODONHSPDROPOFF (Not set)

Default: "40"

--dnahspthreshold <score>

DNA HSP threshold score

Environment variable: $EXONERATE_EXONERATE_DNAHSPTHRESHOLD (Not set)

Default: "75"

--proteinhspthreshold <score>

Protein HSP threshold score

Environment variable: $EXONERATE_EXONERATE_PROTEINHSPTHRESHOLD (Not set)

Default: "30"

--codonhspthreshold <score>

Codon HSP threshold score

Environment variable: $EXONERATE_EXONERATE_CODONHSPTHRESHOLD (Not set)

Default: "50"

--dnawordlimit <score>

Score limit for dna word neighbourhood

Environment variable: $EXONERATE_EXONERATE_DNAWORDLIMIT (Not set)

Default: "0"

--proteinwordlimit <score>

Score limit for protein word neighbourhood

Environment variable: $EXONERATE_EXONERATE_PROTEINWORDLIMIT (Not set)

Default: "4"

--codonwordlimit <score>

Score limit for codon word neighbourhood

Environment variable: $EXONERATE_EXONERATE_CODONWORDLIMIT (Not set)

Default: "4"

--geneseed <threshold>

Geneseed Threshold

Environment variable: $EXONERATE_EXONERATE_GENESEED (Not set)

Default: "0"

--geneseedrepeat <number>

Seeds per diagonal required for geneseed HSP seeding

Environment variable: $EXONERATE_EXONERATE_GENESEEDREPEAT (Not set)

Default: "3"

Alignment options:

-----------------

--alignmentwidth

Alignment display width

Environment variable: $EXONERATE_EXONERATE_ALIGNMENTWIDTH (Not set)

Default: "80"

--forwardcoordinates

Report all coordinates on the forward strand

Environment variable: $EXONERATE_EXONERATE_FORWARDCOORDINATES (Not set)

Default: "TRUE"

SAR Options:

-----------

--quality <percent>

HSP quality threshold

Environment variable: $EXONERATE_EXONERATE_QUALITY (Not set)

Default: "0"

Splice Site Prediction Options:

------------------------------

--splice3

Supply frequency matrix for 3' splice sites

Environment variable: $EXONERATE_EXONERATE_SPLICE3 (Not set)

Default: "primate"

--splice5

Supply frequency matrix for 5' splice sites

Environment variable: $EXONERATE_EXONERATE_SPLICE5 (Not set)

Default: "primate"

--forcegtag

Force use of gt...ag splice sites

Environment variable: $EXONERATE_EXONERATE_FORCEGTAG (Not set)

Default: "FALSE"

--

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