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Old 11-09-2012, 12:17 PM   #1
andtill
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Location: Sweden

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

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
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Old 11-09-2012, 12:49 PM   #2
joshuapk
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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)
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