BLAST+中blastn参数详解

【转】BLAST+中blastn参数详解

2012-05-22 13:25

转载自  lidaof

最终编辑  lidaof

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 -db database_name -query input_file -out output_file -evalue evalue -max_target_seqs num_sequences -num_threads int_value -outfmt format format_string blastn -db database_name -query input_file -out output_file -evalue evalue -max_target_seqs num_sequences -num_threads int_value -outfmt format "7 qacc sacc evalue length pident" 例如： blastn -db plant_rna -query test.fa -out test.out -evalue 0.00001 -max_target_seqs 5 -num_threads 4 -outfmt format "7 qacc sacc evalue length pident" 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_seqs:设置最多的目标序列匹配数（以前我都用-b 5 -v 5,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） -outfmt format "7 qacc sacc evalue length pident" ：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parser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： *** Formatting options -outfmt    alignment view options:      0 = pairwise,      1 = query-anchored showing identities,      2 = query-anchored no identities,      3 = flat query-anchored, show identities,      4 = flat query-anchored, no identities,      5 = XML Blast output,      6 = tabular,      7 = tabular with comment lines,      8 = Text ASN.1,      9 = Binary ASN.1     10 = Comma-separated values    Options 6, 7, and 10 can be additionally configured to produce    a custom format specified by space delimited format specifiers.    The supported format specifiers are:                When not provided, the default value is:    'qseqid sseqid pident length mismatch gapopen qstart qend sstart send    evalue bitscore', which is equivalent to the keyword '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_search_strategy filename]     [-export_search_strategy filename] [-task task_name] [-db database_name]     [-dbsize num_letters] [-gilist filename] [-negative_gilist filename]     [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]     [-subject subject_input_file] [-subject_loc range] [-query input_file]     [-out output_file] [-evalue evalue] [-word_size int_value]     [-gapopen open_penalty] [-gapextend extend_penalty]     [-perc_identity float_value] [-xdrop_ungap float_value]     [-xdrop_gap float_value] [-xdrop_gap_final float_value]     [-searchsp int_value] [-penalty penalty] [-reward reward] [-no_greedy]     [-min_raw_gapped_score int_value] [-template_type type]     [-template_length int_value] [-dust DUST_options]     [-filtering_db filtering_database]     [-window_masker_taxid window_masker_taxid]     [-window_masker_db window_masker_db] [-soft_masking soft_masking]     [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]     [-best_hit_score_edge float_value] [-window_size int_value]     [-off_diagonal_range int_value] [-use_index boolean] [-index_name string]     [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]     [-outfmt format] [-show_gis] [-num_descriptions int_value]     [-num_alignments int_value] [-html] [-max_target_seqs num_sequences]     [-num_threads int_value] [-remote] [-version] DESCRIPTION    Nucleotide-Nucleotide BLAST 2.2.23+ OPTIONAL ARGUMENTS -h    Print USAGE and DESCRIPTION; ignore other arguments -help    Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments -version    Print version number; ignore other arguments *** Input query options -query    Input file name    Default = `-' -query_loc    Location on the query sequence (Format: start-stop) -strand    Query strand(s) to search against database/subject    Default = `both' *** General search options -task                 'megablast' 'vecscreen' >    Task to execute    Default = `megablast' -db    BLAST database name     * Incompatible with: subject, subject_loc -out    Output file name    Default = `-' -evalue    Expectation value (E) threshold for saving hits    Default = `10' -word_size =4>    Word size for wordfinder algorithm (length of best perfect match) -gapopen    Cost to open a gap -gapextend    Cost to extend a gap -penalty    Penalty for a nucleotide mismatch -reward =0>    Reward for a nucleotide match -use_index    Use MegaBLAST database index -index_name    MegaBLAST database index name *** BLAST-2-Sequences options -subject    Subject sequence(s) to search     * Incompatible with: db, gilist, negative_gilist, db_soft_mask -subject_loc    Location on the subject sequence (Format: start-stop)     * Incompatible with: db, gilist, negative_gilist, db_soft_mask, remote *** Formatting options -outfmt    alignment view options:      0 = pairwise,      1 = query-anchored showing identities,      2 = query-anchored no identities,      3 = flat query-anchored, show identities,      4 = flat query-anchored, no identities,      5 = XML Blast output,      6 = tabular,      7 = tabular with comment lines,      8 = Text ASN.1,      9 = Binary ASN.1     10 = Comma-separated values    Options 6, 7, and 10 can be additionally configured to produce    a custom format specified by space delimited format specifiers.    The supported format specifiers are:             qseqid means Query Seq-id                qgi means Query GI               qacc means Query accesion             sseqid means Subject Seq-id          sallseqid means All subject Seq-id(s), separated by a ';'                sgi means Subject GI             sallgi means All subject GIs               sacc means Subject accession            sallacc means All subject accessions             qstart means Start of alignment in query               qend means End of alignment in query             sstart means Start of alignment in subject               send means End of alignment in subject               qseq means Aligned part of query sequence               sseq means Aligned part of subject sequence             evalue means Expect value           bitscore means Bit score              score means Raw score             length means Alignment length             pident means Percentage of identical matches             nident means Number of identical matches           mismatch means Number of mismatches           positive means Number of positive-scoring matches            gapopen means Number of gap openings               gaps means Total number of gaps               ppos means Percentage of positive-scoring matches             frames means Query and subject frames separated by a '/'             qframe means Query frame             sframe means Subject frame    When not provided, the default value is:    'qseqid sseqid pident length mismatch gapopen qstart qend sstart send    evalue bitscore', which is equivalent to the keyword 'std'    Default = `0' -show_gis    Show NCBI GIs in deflines? -num_descriptions =0>    Number of database sequences to show one-line descriptions for    Default = `500' -num_alignments =0>    Number of database sequences to show alignments for    Default = `250' -html    Produce HTML output? *** Query filtering options -dust    Filter query sequence with DUST (Format: 'yes', 'level window linker', or    'no' to disable)    Default = `20 64 1' -filtering_db    BLAST database containing filtering elements (i.e.: repeats) -window_masker_taxid    Enable WindowMasker filtering using a Taxonomic ID -window_masker_db    Enable WindowMasker filtering using this repeats database. -soft_masking    Apply filtering locations as soft masks    Default = `true' -lcase_masking    Use lower case filtering in query and subject sequence(s)? *** Restrict search or results -gilist    Restrict search of database to list of GI's     * Incompatible with: negative_gilist, remote, subject, subject_loc -negative_gilist    Restrict search of database to everything except the listed GIs     * Incompatible with: gilist, remote, subject, subject_loc -entrez_query    Restrict search with the given Entrez query     * Requires: remote -db_soft_mask    Filtering algorithm ID to apply to the BLAST database as soft masking     * Incompatible with: subject, subject_loc -perc_identity    Percent identity -culling_limit =0>    If the query range of a hit is enveloped by that of at least this many    higher-scoring hits, delete the hit     * Incompatible with: best_hit_overhang, best_hit_score_edge -best_hit_overhang =0 and =<0.5)>    Best Hit algorithm overhang value (recommended value: 0.1)     * Incompatible with: culling_limit -best_hit_score_edge =0 and =<0.5)>    Best Hit algorithm score edge value (recommended value: 0.1)     * Incompatible with: culling_limit -max_target_seqs =1>    Maximum number of aligned sequences to keep *** Discontiguous MegaBLAST options -template_type    Discontiguous MegaBLAST template type     * Requires: template_length -template_length    Discontiguous MegaBLAST template length     * Requires: template_type *** Statistical options -dbsize    Effective length of the database -searchsp =0>    Effective length of the search space *** Search strategy options -import_search_strategy    Search strategy to use     * Incompatible with: export_search_strategy -export_search_strategy    File name to record the search strategy used     * Incompatible with: import_search_strategy *** Extension options -xdrop_ungap    X-dropoff value (in bits) for ungapped extensions -xdrop_gap    X-dropoff value (in bits) for preliminary gapped extensions -xdrop_gap_final    X-dropoff value (in bits) for final gapped alignment -no_greedy    Use non-greedy dynamic programming extension -min_raw_gapped_score    Minimum raw gapped score to keep an alignment in the preliminary gapped and    traceback stages -ungapped    Perform ungapped alignment only? -window_size =0>    Multiple hits window size, use 0 to specify 1-hit algorithm -off_diagonal_range =0>    Number of off-diagonals to search for the 2nd hit, use 0 to turn off    Default = `0' *** Miscellaneous options -parse_deflines    Should the query and subject defline(s) be parsed? -num_threads =1>    Number of threads to use in the BLAST search    Default = `1'     * Incompatible with: remote -remote    Execute search remotely?     * Incompatible with: gilist, negative_gilist, subject_loc, num_threads