The genomes and assemblies searched were N. vectensis (JGI 1.0), D. melanogaster (BDGP 5), T. castaneum (Baylor 2.0), C. teleta (JGI 1.0), B. floridae (JGI 2.0), Homo sapiens (NCBI36), C. intestinalis (JGI 2.0) and C. elegans (Wormbase WS200).
The different categories of violations include mob violence, criminal prosecution, violations of the right of assembly, search and seizure issues, the mis-treatment of conscientious objectors, and loss of employment because of political views.
All known and predicted Tetherin gene sequences in mammals were obtained by protein databases or genome assembly searches.
The test/evaluation was divided into the following steps: application assembly, search, and view, insertion and update of data.
Before the assembly search, adaptors, polyA tails, low quality sequences, short sequences less than 100 bp in length, and vector sequences were removed.
The frequency of loss or gain of copy number described in the DGV (UCSC Genome Browser and GRCh37/hg19 assembly, search performed on 29 May 2014) is presented in Additional file 1: Table S2 [ 4, 6, 35].
Due to the short size of contigs of the shark genome assembly searches were carried out using the coding sequence of the human and zebrafish PTHRs transmembrane (TM) domains retrieved from PRINTs database (http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/).
The sequences of the D. melanogaster probes were predicted by blasting primers from the D. melanogaster probe (GEO Profiles accession: GPL6056) against the D. melanogaster Release 5 assembly and searching for unique and proximal (within 600 base pairs of each other) targets.
To evaluate the gene representation of our assemblies, we searched each assembly for sequence similarity with a core set of conserved eukaryotic genes (CEGMA) (Parra et al. 2007) and with gene models from sequenced anthozoan genomes: the coral A. digitifera (OIST: adi_v1.0.1) (Shinzato et al. 2011) and the anemone N. vectensis (assembly version: Nemve1) (Putnam et al. 2007).
To determine the putative gene identities, unique consensus sequences from the all catfish reference assembly and de novo assembly were searched against the Uniprot database and NCBI zebrafish Refseq protein database using BLASTX with a cutoff E-value of 1E-10.
