Identification of copepod gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project)

<p>Field collected copepod gut content sequences were identified&nbsp;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 <a href=\"http://dmoserv3.bco-dmo.org/data_docs/Food_limits_copepod_nauplii/nauplii_gutcontent_sequence.pdf\" target=\"_blank\">nauplii_gutcontent_sequence.pdf</a> 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.</p>

<p><strong>Related Reference:</strong></p>

<p>* 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</p>

野外采集的桡足类肠道内含物序列，可通过与本地桡足类物种序列文库比对，或采用序列相似性分析方法完成物种鉴定。序列比对采用美国国家生物技术信息中心（National Center for Biotechnology Information, NCBI）提供的web_blast.pl脚本执行（链接：http://ncbi.nlm.nih.gov/blast/docs/web_blast.pl）。我们自行编写Perl脚本处理BLAST（碱基局部比对搜索工具）输出结果，以提取比对命中序列的登录号；随后通过NCBI的Batch Entrez工具（链接：http://www.ncbi.nlm.nih.gov/sites/batchentrez），利用该登录号获取完整的序列记录，并从记录中提取分类学信息。上述分析流程的程序输出结果可参见nauplii_gutcontent_sequence.pdf（链接：http://dmoserv3.bco-dmo.org/data_docs/Food_limits_copepod_nauplii/nauplii_gutcontent_sequence.pdf）。随后，我们比对得分前10%的BLAST结果的分类学信息，将序列注释至所有高得分比对命中共有的最低分类学层级。

**相关参考文献：**
* Craig, Carrie、Wim J. Kimmerer及C. Sarah Cohen，2014年。一种用于研究桡足类无节幼体摄食行为的DNA检测方法。《浮游生物研究期刊》（Journal of Plankton Research），36卷第1期：271-275