Suppose I have sequence with its header as follows:
>gi|283509329|gb|GU327626.1| Candida olivae strain ATCC MYA-4568 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 26S ribosomal RNA gene, partial sequence
TTTCCGTAGGTGAACCTGCGGAAGGATCATTACAGTTAGTTTTAGTTCTATTGCCTGCGCTTAATTGCGC
GGCGATGAACAAACACCTTACACACTGTGTTTTTGTTTTTTTGAAAACTTGCTTTGGTTTGGCGCAAGCT
GGGCCAAAGACTACACTTAAACTTCAATTGTGAAATTGAATTGTTTTTAAATTTTTGTCAATTTTGTTTG
ATTAATTTCAAAATAATCTTCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCA
GCGAAATGCGATAAGTAATATGAATTGCAGATTTTCGTGAATCATCGAATCTTTGAACGCACATTGCGGC
CTCTGGTATTCCAGAGGCCATGCCTGTTTGAGCGTCATTTCTCTCTCAAACCTTTGGGTTTGGTATTGAG
TGATACTCTTAGTCGGACTAAGCGTTTGCTTGAAATATAACGGCATGAGCGTACTGGATAGTACGAACTA
GTTTTTCAATGTATTAGGTTTATCCAACTCGTTGAAGCAACTGGGGAAGTAAATTTCTAGTAATTTGGCT
TGGCCTTATAACAACAAACATAAGTTTGACCTCAAATCAGGTGAGATTACCCGCTGAACTTAAGCATATC
AA
What i need to extract is species, genus and strain from the above header description
Please i need to do it aspa. Any suggesstion??
I tried using Bio::DB::Taxonomy with codes below
$db=Bio::DB::Taxonomy->new(-source=>'entrez');
$gi=283509329;
$node = $db->get_Taxonomy_Node(-gi=>$gi, -db=>'Nucleotide');
Then i tried doing $node->species; // it say can't locate it..blah blah
Please help me out if there is any solution to it?
Thanks
