©2020 Biological and Chemical Oceanography Data Management Office.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
Kimmerer, W., Cohen, S. (2021) Identification of copepod gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2021-06-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/546723 [access date]
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