Question: Querying blast and getting raw hit fasta sequence
0
gravatar for ishengomae
5.8 years ago by
ishengomae100
Tanzania, United Republic Of
ishengomae100 wrote:

I have downloaded refseq_rna database and I want to query this database on my standalone blast with tblastn. I have many queries and what I want to achieve is to not only get blast alignments but also to get the entire length of the hit sequences that produced the alignments. Can somebody suggest to me a simpler way of doing this? I am happy to elaborate further in case more clarification is needed.

blast alignment sequence • 2.1k views
ADD COMMENTlink modified 5.8 years ago by 5heikki8.7k • written 5.8 years ago by ishengomae100
0
gravatar for 5heikki
5.8 years ago by
5heikki8.7k
Finland
5heikki8.7k wrote:

Parse the Subject IDs to a list and extract them from your db with blastdbcmd -entry_batch

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by 5heikki8.7k

Done. Thanks very much.

ADD REPLYlink written 5.8 years ago by ishengomae100
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