Extract fasta from BLAST hits

Question

[biotech]

I would like to extract fasta nucleotide from BLAST hits. I'm trying to get the synthetic region of a protein.

I'm BLASTing via BLASTn the query gene and their 5' and 3' genes against a database of bacterial genomes. The database contains 200 genomes and I need to have fasta sequence of the query gene and their 5' and 3' genes in a separated file for each strain.

Some problems are that this protein is sometimes unassembled, so hits will be in two contigs and thus I will have to parse also the second best BLAST hit.

I'm open to new alternatives is this one seems not appropriate.

Thanks!

[biotech]

Maybe an alternative would be to parse selected genomic regions from a multiple genome alignment of the 200 strains? A caveat is that an alignment like this one will sure crash.

[5heikki]

That's what I would do. Tabular output and then with blastdbcmd..

 -entry_batch <File_In>
   Input file for batch processing (Format: one entry per line, seq id
   followed by optional space-delimited specifier(s)
   [range|strand|mask_algo_id]

[biotech]

Here hits were parsed in fasta format but using BLASTp and only one protein as a query. The difference is that I'm trying to get nucleotide sequence for adjacent 5' and 3' genes too. Taking Only Aligned Sequences In A Blast