How do you get the entire corresponding gene after a blast search via blast+?

Question

[eightpints]

How do I get the entire gene that a blast search produces?

For example, when I blast a gene in nr and get the result, I am only given the start and stop positions of the blast result in the genome. That result is included in a specific gene in the genome. How do I used blast+ to extract the entire gene from a genome and not just the part that matched in blast?

Answer 1

[Peter]

You could use blastdbcmd to extract the matching sequence from the BLAST database you searched against.

[eightpints]

But when I use blastdbcmd and specify the range, I still only know the range of the blast result and not the whole gene.

[Peter]

Use blastdbcmd WITHOUT specifying a range, and it gives you the full sequence of the hit.

If the database was made up of gene sequences or similar (short) sequences, this is good. If the database was built of whole genomes or contigs, these pieces might be bigger than you wanted..