if you're using the blast+ version : use the blastdbcmd utility (comes with the blast installation) to retrieve sequences from the blastDBs , either use '-entry <id>' for a single sequence or '-entry_batch <file>' for a whole list of IDs . You'll still have to first get the list of IDs you want to retrieve as suggested by st.ph.n

Another method:

1. Use option -outfmt 5 in BLAST+ suite command line. This will give you a xml file as output.

2. Use this little python script to parse rapidly data.

    import re
   
    output = open('file.out','w')
    n = 0
    print >> output, 'protein'+'\t'+'hit_def'+'\t'+'hit_acc'+'\t'+'e-value'
   
    with open('blast_output.xml','r') as xml:
    for line in xml:
       if re.search('<Iteration_query-def>', line) != None:
           n = n + 1
           line = line.strip()
           line = line.rstrip()
           line = line.strip('<Iteration_query-def>')
           line = line.rstrip('</')
           query_def = line
       if re.search('No hits found', line) != None:
           line = line.strip()
           line = line.rstrip()
           line = line.strip('<Iteration_message>')
           line = line.rstrip('</')
           print n
           print >> output, query_def+'\t'+line
       if re.search('<Hit_def>', line) != None:
           line = line.strip()
           line = line.rstrip()
           line = line.strip('<Hit_def>')
           line = line.rstrip('</')
           hit_def = line
       if re.search('<Hit_accession>', line) != None:
           line = line.strip()
           line = line.rstrip()
           line = line.strip('<Hit_accession>')
           line = line.rstrip('</')
           hit_acc = line       
       if re.search('<Hsp_evalue>', line) != None:
           line = line.strip()
           line = line.rstrip()
           line = line.strip('<Hsp_evalue>')
           line = line.rstrip('</')
           e_val = line
           print n
           print >> output, query_def+'\t'+hit_def+'\t'+hit_acc+'\t'+e_val 
   
    output.close()
   

This step will give you a pretty file with proteins, hit name, acession number of hit and e-value as columns. This file can be also parsed easily.

Thanks!

I created something like that and it seems to work (for me:) ).

https://github.com/mmagnus/rna-pdb-tools/tree/master/rna_pdb_tools/utils/rna_seq_search_BLASTn_outfmt-6

Best