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Old 11-03-2012, 12:26 PM   #1
oliviaxinw
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Location: Massachussets

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Default Mapping species name back to taxonomy database to get higher taxonomic classification

Hi,

I'm new to bioinformatics and have a problem with getting taxonomic information for my contig database.

Currently I have a file that has all the contigs IDs with their taxonomic assignment to the species level as the output of an annotation pipeline. However, for another analysis, I want to group all the contigs by their higher taxonomic level, like family or order. How can I retrieve the higher taxonomic information through the species names?

Does anyone know a tool that can map the species name to NCBI taxonomy database and output the higher taxonomic level name information?

For example, when the input is Escherichia coli, the output would be: (in a table), Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Escherichia.

Thanks.
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Old 11-04-2012, 12:19 AM   #2
Cedric Woods
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Location: New Zealand

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Smile Higher Taxonomic Classification

Hi Olivia
Try www.biolists.com.
It's new, so the database needs pumping up, but basic higher classification is available - mostly from Genus-level searches, otherwise from Families. The aim is all species with Common Names!
Cheers, Cedric
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Old 10-27-2015, 07:56 AM   #3
fibar
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Location: Argentina

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Hi,
Old thread, but I'm also interested in Olivia's topic.
This is typical for a metagenomic data set.
I did not see bacterial names at BioLists, suggested by Cedric.
Any other help?
Thanks.
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