Dataset: 5d_molecular id of copepod guts
Deployment: Kimmerer_2013

Identification of copepod gut contents
Principal Investigator: 
William Kimmerer (San Francisco State University, SFSU-RTC)
Co-Principal Investigator: 
Sarah Cohen (San Francisco State University, SFSU-RTC)
BCO-DMO Data Manager: 
Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)
Project: 
Current State: 
Final no updates expected
Version: 
2015-01-15
Version Date: 
2015-01-15
Description

Field collected copepod gut content sequences were identified either by comparison to our sequence library of local copepod species or using a sequence similarity approach. Sequences were Blasted using NCBI’s web_blast.pl script (http://ncbi.nlm.nih.gov/blast/docs/web_blast.pl). The Blast output was manipulated with perl scripts we wrote to isolate the accession numbers for the BLAST hits, use the accession numbers to get the full records using NCBI’s Batch Entrez (http://www.ncbi.nlm.nih.gov/sites/batchentrez), and get the taxonomic information from the full records. See nauplii_gutcontent_sequence.pdf for the output of these programs. We then compared the taxonomic information among the top 10% BLAST scores to assign the sequence to the lowest, taxonomic level shared by the top scoring hits.

Related Reference:

* Craig, Carrie, Wim J. Kimmerer, and C. Sarah Cohen. 2014. A DNA-based method for investigating feeding by copepod nauplii. Journal of Plankton Research 36 (1): 271-275

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