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. 2014 May 28;15(1):406. doi: 10.1186/1471-2164-15-406

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© Sanders et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Venn diagram displaying the number of transcripts annotated by each method. Gene Ontology terms were added with Blast2GO using the BLASTX algorithm against NCBI’s nr protein database and a threshold of 1 × 10^-03. A set of conserved eukaryotic genes was identified with CEGMA. HMM protein families from the PFAM and TIGR databases were assigned to the amino acid translation of the most likely reading frame for each transcript (identified using an open reading frame prediction tool) using HMMscan under default settings. HMMscan annotations were constrained to a significance threshold of 0.01. Orthogroups were assigned to the same amino acid translations using the orthoMCL web server.