Automatic resolution of sequence identifiers
The BLAST+ search applications support automatic resolution of query and subject sequence identifiers specified as GIs or accessions (see the cookbook section for an example). This feature enables the user to specify one or more sequence identifiers (GIs and/or accessions, one per line) in a file as the input to the -query and -subject command line options. Upon encountering this type of input, by default the BLAST+ search applications will try to resolve these sequence identifiers in locally available BLAST databases first, then in the BLAST databases at NCBI, and finally in Genbank (the latter two data sources require a properly configured internet connection). These data sources can be configured via the DATA_LOADERS configuration option and the BLAST databases to search can be configured via the BLASTDB_PROT_DATA_LOADER and BLASTDB_NUCL_DATA_LOADER configuration options (see the section on Configuring BLAST).
自動分辨序列標(biāo)識符
BLAST +搜索應(yīng)用程序支持自動解析指定為GI或加入的查詢和主題序列標(biāo)識符（有關(guān)示例辕近，請參閱coobook 部分）。 此功能使用戶能夠在文件中指定一個或多個序列標(biāo)識符（GI和/或入口焙畔，每行一個）作為-query和-subject命令行選項的輸入前酿。
在遇到這種類型的輸入時灾部，默認(rèn)情況下际乘，BLAST +搜索應(yīng)用程序?qū)⑹紫葒L試在本地可用的BLAST數(shù)據(jù)庫中解析這些序列標(biāo)識符诺核，然后在NCBI的BLAST數(shù)據(jù)庫中，最后在Genbank中（后兩個數(shù)據(jù)源需要正確配置的互聯(lián)網(wǎng) 連接）若专。 可以通過DATA_LOADERS配置選項配置這些數(shù)據(jù)源许蓖，并且可以通過BLASTDB_PROT_DATA_LOADER和BLASTDB_NUCL_DATA_LOADER配置選項來配置要搜索的BLAST數(shù)據(jù)庫（請參閱配置BLAST部分）。
本地化數(shù)據(jù)庫：http://wangyufeng222.blog.163.com/blog/static/12822207020101013105158335/
參考：http://blog.sciencenet.cn/blog-981687-725295.html
格式化數(shù)據(jù)庫
makeprofiledb -title Pfam.v.xxx -in Pfam.pn -out Pfam -threshold 9.82 -scale 100.0 -dbtype rps -index true
source .bashrc
blastp
blastp -query '/home/huangle/data/1.fas' -out '/home/huangle/data/out.txt' -task 'blastp' -db 'Cdd'
huangle@huangle-ThinkStation-P300:~/CDD/cdd$
rpsblast
rpsblast -query '/home/huangle/data/1.fas' -out '/home/huangle/data/out-rpsblast1.txt' -db '/home/huangle/data/cdd/Cdd' -evalue '1e-23' -outfmt 7
rpsblast -query '/home/huangle/data/1.fas' -out '/home/huangle/data/out-rpsblast.txt' -db Cdd -evalue 1e-23
我的sh文件:
rpsblast.sh 有點(diǎn)慢
rpsblast -query '/home/huangle/data/1.fas' -out '/home/huangle/data/out-rpsblast1.txt' -db '/home/huangle/data/cdd/Cdd' -evalue '1e-23' -outfmt 7
