1 软件下载

如果网页下载或迅雷下载会导致下载不完整，安装出错。

安装出错.png

命令行下载：

$client=new-object System.Net.WebClient
$client.DownloadFile('ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.12.0+-win64.exe','E:\Download')

 wget -c ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.12.0+-win64.exe

下载界面.png

需要先安装wget软件
或者百度网盘下载，留言获取。
安装好后测试。

系统变量查看.jpg

通过命令提示符转到命令行，或者SHIFT+鼠标右键，在此处打开Powershell窗口

blastp -h

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] [-negative_seqidlist filename]
    [-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
    [-negative_taxidlist filename] [-ipglist filename]
    [-negative_ipglist 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] [-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] [-sorthits sort_hits]
    [-sorthsps sort_hsps] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-mt_mode int_value] [-ungapped] [-remote]
    [-comp_based_stats compo] [-use_sw_tback] [-version]

DESCRIPTION
   Protein-Protein BLAST 2.12.0+

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

2.构建本地数据库

makeblastdb -help

USAGE
  makeblastdb.exe [-h] [-help] [-in input_file] [-input_type type]
    -dbtype molecule_type [-title database_title] [-parse_seqids]
    [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
    [-mask_desc mask_algo_descriptions] [-gi_mask]
    [-gi_mask_name gi_based_mask_names] [-out database_name]
    [-blastdb_version version] [-max_file_sz number_of_bytes]
    [-logfile File_Name] [-taxid TaxID] [-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
   Application to create BLAST databases, version 2.12.0+

REQUIRED ARGUMENTS
 -dbtype <String, `nucl', `prot'>
   Molecule type of target db

OPTIONAL ARGUMENTS
 -h
   Print USAGE and DESCRIPTION;  ignore all other parameters
 -help
   Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
 -version
   Print version number;  ignore other arguments

 *** Input options
 -in <File_In>
   Input file/database name
   Default = `-'
 -input_type <String, `asn1_bin', `asn1_txt', `blastdb', `fasta'>
   Type of the data specified in input_file
   Default = `fasta'

 *** Configuration options
 -title <String>
   Title for BLAST database
   Default = input file name provided to -in argument
 -parse_seqids
   Option to parse seqid for FASTA input if set, for all other input types
   seqids are parsed automatically
 -hash_index
   Create index of sequence hash values.

 *** Sequence masking options
 -mask_data <String>
   Comma-separated list of input files containing masking data as produced by
   NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)
 -mask_id <String>
   Comma-separated list of strings to uniquely identify the masking algorithm
    * Requires:  mask_data
    * Incompatible with:  gi_mask
 -mask_desc <String>
   Comma-separated list of free form strings to describe the masking algorithm
   details
    * Requires:  mask_id
 -gi_mask
   Create GI indexed masking data.
    * Requires:  parse_seqids
    * Incompatible with:  mask_id
 -gi_mask_name <String>
   Comma-separated list of masking data output files.
    * Requires:  mask_data, gi_mask

 *** Output options
 -out <String>
   Name of BLAST database to be created
   Default = input file name provided to -in argumentRequired if multiple
   file(s)/database(s) are provided as input
 -blastdb_version <Integer, 4..5>
   Version of BLAST database to be created
   Default = `5'
 -max_file_sz <String>
   Maximum file size for BLAST database files
   Default = `1GB'
 -logfile <File_Out>
   File to which the program log should be redirected

 *** Taxonomy options
 -taxid <Integer, >=0>
   Taxonomy ID to assign to all sequences
    * Incompatible with:  taxid_map
 -taxid_map <File_In>
   Text file mapping sequence IDs to taxonomy IDs.
   Format:<SequenceId> <TaxonomyId><newline>
    * Requires:  parse_seqids
    * Incompatible with:  taxid

构建索引文件

蛋白

makeblastdb -in uniprot-proteome_UP000000549.fasta -parse_seqids -hash_index -dbtype prot -out library

uniprot-proteome_UP000000549.fasta为比对到的氨基酸序列

核酸

makeblastdb -in genome.fa -dbtype nucl -out library -parse_seqids

genome.fa为要比对的基因组
构建完会出现以library为前缀的13个文件

3 序列比对

blastp -query test.fasta -db library -out test.txt
blastp -query test.fasta -out blast.txt -db library  -num_threads 4  -evalue 1e-10 -best_hit_score_edge 0.05 -best_hit_overhang 0.25 -outfmt 7 -max_target_seqs 1