blast

BLAST+中blastn参数详解

【转】BLAST+中blastn参数详解

2012-05-2213:25

转载⾃

最终编辑

与之前的blast相⽐，新的blast+将blastn,blastx等合作与blastall命令分隔开来，对各个命令的参数定制更加⽅便

个⼈在使⽤blastn的过程中总结了⼀些⾃认为常⽤的参数，总结如下：

blastn-dbdataba_name-queryinput_file-outoutput_file-evalueevalue-max_target_qsnum_quences-num_threadsint_value-

outfmtformatformat_string

blastn-dbdataba_name-queryinput_file-outoutput_file-evalueevalue-max_target_qsnum_quences-num_threadsint_value-

outfmtformat"7qaccsaccevaluelengthpident"

例如：

blastn-dbplant_-evalue0.00001-max_target_qs5-num_threads4-outfmtformat"7qaccsaccevalue

lengthpident"

blastn:这个不⽤说了吧，核酸对核酸的⽐对

-db:指定blast搜索⽤的数据库，详见上篇⽂章

-query:⽤来查询的输⼊序列，fasta格式

-out：输出结果⽂件

-evalue:设置e值cutoff

-max_target_qs:设置最多的⽬标序列匹配数（以前我都⽤-b5-v5,理解不对请指教）

-num_threads：指定多少个cpu运⾏任务（依赖于你的系统，同于以前的-a参数）

-outfmtformat"7qaccsaccevaluelengthpident"：这个是新BLAST+中最拉风的功能了，直接控制输出格式，不⽤再⽤parr啦，7表

⽰带注释⾏的tab格式的输出，可以⾃定义要输出哪些内容，⽤空格分格跟在7的后⾯，并把所有的输出控制⽤双引号括起来，其中qacc查

询序列的acc,sacc表⽰⽬标序列的acc，evalue即是e值，length即是匹配的长度，pident即是序列相同的百分⽐，其他可⽤的特征（红⾊

字体）如下：

***Formattingoptions

-outfmt

alignmentviewoptions:

0=pairwi,

1=query-anchoredshowingidentities,

2=query-anchorednoidentities,

3=flatquery-anchored,showidentities,

4=flatquery-anchored,noidentities,

5=XMLBlastoutput,

6=tabular,

7=tabularwithcommentlines,

8=TextASN.1,

9=BinaryASN.1

10=Comma-paratedvalues

Options6,7,and10canbeadditionallyconfiguredtoproduce

acustomformatspecifiedbyspacedelimitedformatspecifiers.

Thesupportedformatspecifiersare:

Whennotprovided,thedefaultvalueis:

'qqidsqidpidentlengthmismatchgapopenqstartqendsstartnd

evaluebitscore',whichiquivalenttothekeyword'std'

Default=`0'

调⽤blastn合作加-help参数可以打印出下⾯详细的帮助信息

blastn-help

blastn[-h][-help][-import_arch_strategyfilename]

[-export_arch_strategyfilename][-tasktask_name][-dbdataba_name]

[-dbsizenum_letters][-gilistfilename][-negative_gilistfilename]

[-entrez_queryentrez_query][-db_soft_maskfiltering_algorithm]

[-subjectsubject_input_file][-subject_locrange][-queryinput_file]

[-subjectsubject_input_file][-subject_locrange][-queryinput_file]

[-outoutput_file][-evalueevalue][-word_sizeint_value]

[-gapopenopen_penalty][-gapextendextend_penalty]

[-perc_identityfloat_value][-xdrop_ungapfloat_value]

[-xdrop_gapfloat_value][-xdrop_gap_finalfloat_value]

[-archspint_value][-penaltypenalty][-rewardreward][-no_greedy]

[-min_raw_gapped_scoreint_value][-template_typetype]

[-template_lengthint_value][-dustDUST_options]

[-filtering_dbfiltering_databa]

[-window_masker_taxidwindow_masker_taxid]

[-window_masker_dbwindow_masker_db][-soft_maskingsoft_masking]

[-ungapped][-culling_limitint_value][-best_hit_overhangfloat_value]

[-best_hit_score_edgefloat_value][-window_sizeint_value]

[-off_diagonal_rangeint_value][-u_indexboolean][-index_namestring]

[-lca_masking][-query_locrange][-strandstrand][-par_deflines]

[-outfmtformat][-show_gis][-num_descriptionsint_value]

[-num_alignmentsint_value][-html][-max_target_qsnum_quences]

[-num_threadsint_value][-remote][-version]

DESCRIPTION

Nucleotide-NucleotideBLAST2.2.23+

OPTIONALARGUMENTS

-h

PrintUSAGEandDESCRIPTION;ignoreotherarguments

-help

PrintUSAGE,DESCRIPTIONandARGUMENTSdescription;ignoreotherarguments

-version

Printversionnumber;ignoreotherarguments

***Inputqueryoptions

-query

Inputfilename

Default=`-'

-query_loc

Locationonthequeryquence(Format:start-stop)

-strand

Querystrand(s)toarchagainstdataba/subject

Default=`both'

***Generalarchoptions

-task

'megablast''vecscreen'>

Tasktoexecute

Default=`megablast'

-db

BLASTdatabaname

*Incompatiblewith:subject,subject_loc

-out

Outputfilename

Outputfilename

Default=`-'

-evalue

Expectationvalue(E)thresholdforsavinghits

Default=`10'

-word_size=4>

Wordsizeforwordfinderalgorithm(lengthofbestperfectmatch)

-gapopen

Costtoopenagap

-gapextend

Costtoextendagap

-penalty

Penaltyforanucleotidemismatch

-reward=0>

Rewardforanucleotidematch

-u_index

UMegaBLASTdatabaindex

-index_name

MegaBLASTdatabaindexname

***BLAST-2-Sequencesoptions

-subject

Subjectquence(s)toarch

*Incompatiblewith:db,gilist,negative_gilist,db_soft_mask

-subject_loc

Locationonthesubjectquence(Format:start-stop)

*Incompatiblewith:db,gilist,negative_gilist,db_soft_mask,remote

***Formattingoptions

-outfmt

alignmentviewoptions:

0=pairwi,

1=query-anchoredshowingidentities,

2=query-anchorednoidentities,

3=flatquery-anchored,showidentities,

4=flatquery-anchored,noidentities,

5=XMLBlastoutput,

6=tabular,

7=tabularwithcommentlines,

8=TextASN.1,

9=BinaryASN.1

10=Comma-paratedvalues

Options6,7,and10canbeadditionallyconfiguredtoproduce

acustomformatspecifiedbyspacedelimitedformatspecifiers.

Thesupportedformatspecifiersare:

qqidmeansQuerySeq-id

qgimeansQueryGI

qaccmeansQueryaccesion

sqidmeansSubjectSeq-id

sallqidmeansAllsubjectSeq-id(s),paratedbya';'

sgimeansSubjectGI

sallgimeansAllsubjectGIs

saccmeansSubjectaccession

sallaccmeansAllsubjectaccessions

qstartmeansStartofalignmentinquery

qendmeansEndofalignmentinquery

sstartmeansStartofalignmentinsubject

sstartmeansStartofalignmentinsubject

ndmeansEndofalignmentinsubject

qqmeansAlignedpartofqueryquence

sqmeansAlignedpartofsubjectquence

evaluemeansExpectvalue

bitscoremeansBitscore

scoremeansRawscore

lengthmeansAlignmentlength

pidentmeansPercentageofidenticalmatches

nidentmeansNumberofidenticalmatches

mismatchmeansNumberofmismatches

positivemeansNumberofpositive-scoringmatches

gapopenmeansNumberofgapopenings

gapsmeansTotalnumberofgaps

pposmeansPercentageofpositive-scoringmatches

framesmeansQueryandsubjectframesparatedbya'/'

qframemeansQueryframe

sframemeansSubjectframe

Whennotprovided,thedefaultvalueis:

'qqidsqidpidentlengthmismatchgapopenqstartqendsstartnd

evaluebitscore',whichiquivalenttothekeyword'std'

Default=`0'

-show_gis

ShowNCBIGIsindeflines?

-num_descriptions=0>

Numberofdatabaquencestoshowone-linedescriptionsfor

Default=`500'

-num_alignments=0>

Numberofdatabaquencestoshowalignmentsfor

Default=`250'

-html

ProduceHTMLoutput?

***Queryfilteringoptions

-dust

FilterqueryquencewithDUST(Format:'yes','levelwindowlinker',or

'no'todisable)

Default=`20641'

-filtering_db

BLASTdatabacontainingfilteringelements(i.e.:repeats)

-window_masker_taxid

EnableWindowMaskerfilteringusingaTaxonomicID

-window_masker_db

EnableWindowMaskerfilteringusingthisrepeatsdataba.

-soft_masking

Applyfilteringlocationsassoftmasks

Default=`true'

-lca_masking

Ulowercafilteringinqueryandsubjectquence(s)?

***Restrictarchorresults

-gilist

RestrictarchofdatabatolistofGI's

*Incompatiblewith:negative_gilist,remote,subject,subject_loc

-negative_gilist

RestrictarchofdatabatoeverythingexceptthelistedGIs

*Incompatiblewith:gilist,remote,subject,subject_loc

-entrez_query

RestrictarchwiththegivenEntrezquery

*Requires:remote

-db_soft_mask

FilteringalgorithmIDtoapplytotheBLASTdatabaassoftmasking

*Incompatiblewith:subject,subject_loc

-perc_identity

Percentidentity

-culling_limit=0>

Ifthequeryrangeofahitinvelopedbythatofatleastthismany

higher-scoringhits,deletethehit

*Incompatiblewith:best_hit_overhang,best_hit_score_edge

-best_hit_overhang=0and=<0.5)>

BestHitalgorithmoverhangvalue(recommendedvalue:0.1)

*Incompatiblewith:culling_limit

-best_hit_score_edge=0and=<0.5)>

BestHitalgorithmscoreedgevalue(recommendedvalue:0.1)

*Incompatiblewith:culling_limit

-max_target_qs=1>

Maximumnumberofalignedquencestokeep

***DiscontiguousMegaBLASToptions

-template_type

DiscontiguousMegaBLASTtemplatetype

*Requires:template_length

-template_length

DiscontiguousMegaBLASTtemplatelength

*Requires:template_type

***Statisticaloptions

-dbsize

Effectivelengthofthedataba

-archsp=0>

Effectivelengthofthearchspace

***Searchstrategyoptions

-import_arch_strategy

Searchstrategytou

*Incompatiblewith:export_arch_strategy

-export_arch_strategy

Filenametorecordthearchstrategyud

*Incompatiblewith:import_arch_strategy

***Extensionoptions

-xdrop_ungap

X-dropoffvalue(inbits)forungappedextensions

-xdrop_gap

X-dropoffvalue(inbits)forpreliminarygappedextensions

-xdrop_gap_final

X-dropoffvalue(inbits)forfinalgappedalignment

-no_greedy

Unon-greedydynamicprogrammingextension

-min_raw_gapped_score

Minimumrawgappedscoretokeepanalignmentinthepreliminarygappedand

tracebackstages

tracebackstages

-ungapped

Performungappedalignmentonly?

-window_size=0>

Multiplehitswindowsize,u0tospecify1-hitalgorithm

-off_diagonal_range=0>

Numberofoff-diagonalstoarchforthe2ndhit,u0toturnoff

Default=`0'

***Miscellaneousoptions

-par_deflines

Shouldthequeryandsubjectdefline(s)bepard?

-num_threads=1>

NumberofthreadstouintheBLASTarch

Default=`1'

*Incompatiblewith:remote

-remote

Executearchremotely?

*Incompatiblewith:gilist,negative_gilist,subject_loc,num_threads