Tips for blast+ usage

#####Format local databse for blast search

makeblastdb -in input_file.fa -dbtype nucl/prot -out input_file.db

#####Blast short sequences like miRNAs in your database

blastn -query test.fa -db input_file.db -task blastn-short -out test.out \
-strand plus -num_threads 10

#####Run psiblast

#file.fasta is a multipe-sequence alignment file generated by clustralw or others
psiblast -in_msa file.fasta -db input_file.db -out file.out -num_iterations 3 -evalue 20000 -matrix PAM30 -comp_based_stats 0

#####Extract sequences in FATSA format for given name

blastdbcmd -entry NP_172083.1 -db nr #A gi number is also accepted for -entry

#####Set your favorite output format

blastp -query file.fasta -db nr -out file.out -num_threads=8 -outfmt=6 
*qseqid sseqid pident length slen evalue*

#####Generate PSSM

The correct usage for 2.2.23+ is (-subject produces an error which is fixed in 2.2.24+):

psiblast -db blastdb -in_msa alignment.fasta -out_ascii_pssm pssm.txt

And for 2.2.24+ supplying a subject FASTA file works

psiblast -subject oneseq.fasta -in_msa alignment.fasta -out_ascii_pssm pssm.txt

For both approaches, it does not matter if there is one sequence in db/subject or any subset of the alignment sequences. PSSM output is exactly the same. Note that the query needs to be supplied with in_msa in order to genereate a PSSM in one step.

Specially, [MyHits](myhits.isb-sib.ch/) can accept multiple sequence alignment profiles instead of PSSM to invoke PSI-BLAST or HMMER3.

#

http://www.ncbi.nlm.nih.gov/blast/html/sub_matrix.html

CHENTONG
版权声明:本文为博主原创文章,转载请注明出处。
alipay.png WeChatPay.png

CHENTONG

CHENTONG
积微,月不胜日,时不胜月,岁不胜时。凡人好敖慢小事,大事至,然后兴之务之。如是,则常不胜夫敦比于小事者矣!何也?小事之至也数,其悬日也博,其为积也大。大事之至也希,其悬日也浅,其为积也小。故善日者王,善时者霸,补漏者危,大荒者亡!故,王者敬日,霸者敬时,仅存之国危而后戚之。亡国至亡而后知亡,至死而后知死,亡国之祸败,不可胜悔也。霸者之善著也,可以时托也。王者之功名,不可胜日志也。财物货宝以大为重,政教功名者反是,能积微者速成。诗曰:德如毛,民鲜能克举之。此之谓也。

生信宝典文章集锦

### 培训* [生物信息作图系列R、Cytoscape及图形排版和Python编程培训研讨班开课了](http://mp.weixin.qq.com/s/x-DInL34BbKUR-2UD2Ec3g)* [120分的转录组考题,你能得多少](http://mp.weixi...… Continue reading

基因共表达聚类分析及可视化

Published on November 30, 2017

易生信转录组培训第一期总结

Published on November 15, 2017