How do I extract partial sequence data (Fasta) from multiple hits in NCBI nucleotide?

[andtill]

Hi,

I would like to extract DNA sequence data from one gene on the mitochondrion for multiple species. At NCBI nucleotide I can search for "mitochondrion complete" and I will get a large list of a number of sequenced mitochondrion. From these hits I would like to only extract the DNA sequence data from one gene (annotated as "16S ribosomal RNA"). Alternatively, from all hits, extract DNA sequence data between a specified region (same for all hits).

Thanks!
/Andreas

[joshuapk]

I would suggest either downloading the mitochondria Genbank files and parsing with Bio::Perl Feature-Annotation (http://www.bioperl.org/wiki/HOWTO:Feature-Annotation). Or if these genes have individual identifiers from your BLAST you can use
blastcmddb -db [local nt] -entry_batch [file with ids per line] -out (output name)