psiblast生成pssm矩阵及psiblast参数详解

PSI-BLAST : 敏感度更高的蛋白序列与蛋白序列之间的比对：一般用来生成pssm打分矩阵

其常用命令有USAGE
psiblast [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
[-negative_taxidlist filename] [-entrez_query entrez_query]
[-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]
[-subject_besthit] [-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] [-remote] [-comp_based_stats compo]
[-use_sw_tback] [-gap_trigger float_value] [-num_iterations int_value]
[-out_pssm checkpoint_file] [-out_ascii_pssm ascii_mtx_file]
[-save_pssm_after_last_round] [-save_each_pssm] [-in_msa align_restart]
[-msa_master_idx index] [-ignore_msa_master] [-in_pssm psi_chkpt_file]
[-pseudocount pseudocount] [-inclusion_ethresh ethresh]
[-phi_pattern file] [-version]

上述命令详解：

-h 生成简略命令介绍信息
-help 生成详细命令介绍
-query 后面放你要对比的序列名字，改序列必须为fasta格式，且放在\blast\bin 目录下
fasta格式如下

>1AKHA
KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK

-num_iterations 迭代次数 （整数类型一般会放3）
-db 后面放你格式化的数据库名称 如：nr
-out 你希望输出文件名，可任意取名
-out_ascii_pssm 如果你需要生成pssm矩阵，则需要输入此参数，此参数后放pssm矩阵的名字

一个完整的psi-blast命令如下

psiblast -query 1_dp.fasta -db nr -out 1.txt -num_iterations 3 -out_ascii_pssm 1.pssm

得到的pssm矩阵如下