2020-12-09 blastp参数学习

blastp -query insertions.fasta -out insertions.rep.blast -db repbase -outfmt 6 -evalue 1e-5 -num-threads 10 -max-target_seqs 5

分析

blastp 蛋白序列与蛋白序列的对比，自建了数据库，本人用于查找重复序列

USAGE
  blastp [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name] [-db database_name]
    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
    [-negative_gilist filename] [-entrez_query entrez_query]
    [-db_soft_mask filtering_algorithm] [-db_hard_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]
    [-qcov_hsp_perc float_value] [-max_hsps int_value]
    [-xdrop_ungap float_value] [-xdrop_gap float_value]
    [-xdrop_gap_final float_value] [-searchsp int_value]
    [-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking]
    [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]
    [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
    [-window_size int_value] [-lcase_masking] [-query_loc range]
    [-parse_deflines] [-outfmt format] [-show_gis]
    [-num_descriptions int_value] [-num_alignments int_value]
    [-line_length line_length] [-html] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
    [-use_sw_tback] [-version]

DESCRIPTION
   Protein-Protein BLAST 2.5.0+

Use '-help' to print detailed descriptions of command line arguments

[-query input_file] -query 输入需要比对的序列

[-out output_file] -out 输出比对的结果文件

[-db database_name] -db 输入参考的数据库名

[-outfmt format]  -outfmt outformat 输出格式 6 = Tabular,表格

[-evalue evalue]  -evalue <Real>  Expectation value (E) threshold for saving hits 保存点击的期望值（E）阈值 

[-num_threads int_value] -num_threads <Integer, >=1> Number of threads (CPUs) to use in the BLAST search CPUs用于BLAST搜索

[-max_target_seqs num_sequences] -max_target_seqs <Integer, >=1> Maximum number of aligned sequences to keep 最大目标比对序列数

一切参数的详细信息都可以从blastp -help找到

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