1 Ab_initio_RepeatMask Repeats Interspersed repeats and low complexity sequence identified by <a rel="external" href="http://www.repeatmasker.org/">RepeatMasker</a> using ab initio repeat profiles specific to the species.
1 AlignAffy Probes (Affymetrix) Microarray probes from Affymetrix (and other manufacturers) are aligned to the genome by Ensembl, if probe sequences are provided. The mapping is a two-step procedure outlined <a href="/info/about/docs/microarray_probe_set_mapping.html">here</a>.
1 AffyAlign Probes (Affymetrix) Microarray probes from Affymetrix (and other manufacturers) are aligned to the genome by Ensembl, if probe sequences are provided. The mapping is a two-step procedure outlined <a href="/info/about/docs/microarray_probe_set_mapping.html">here</a>.
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1 FANTOM_GIS_PET Fantom GIS ditags These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel="external" href="http://fantom.gsc.riken.go.jp/">Riken Fantom</a> project and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 FANTOM_GIS_PET_raw FANTOM GIS ditags raw These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel="external" href="http://fantom.gsc.riken.go.jp/">Riken Fantom</a> project and aligned to the genome using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>.
1 Fgenesh Gene prediction (FGENESH) Ab initio prediction of protein coding genes, based on the genomic sequence alone <a rel="external" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10779491">AA Salamov et al., Genome Res. 2000 4:516-22</a>.
1 FirstEF First exon finder First Exon Finder (<a rel="external"href="http://www.nature.com/ng/journal/v29/n4/full/ng780.html">First EF</a>) predicts positions of the first exons of transcripts, both coding and non-coding, using the sequence to identify features such as CpG islands and promoter regions.
1 GID Gene prediction (geneid) Ab initio prediction of protein coding genes by <a rel="external" href="http://www1.imim.es/software/geneid/">Geneid</a>, with parameters customised for accuracy in Tetraodon sequences.
1 GSC Gene prediction (Genscan) Ab initio prediction of protein coding genes by <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45VGF7T-9&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=aa15a5f8122912c172ddb9dd15b237dc">Genscan</a>, with parameters customised for accuracy in Tetraodon sequences
1 GSTEN Genes (Genoscope) Genes were annotated by <a rel="external" href="http://www.genoscope.cns.fr/spip/">Genoscope</a>, combining evidence from <a rel="external" href="http://www1.imim.es/software/geneid/">Geneid</a>, <a rel="external" href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45VGF7T-9&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=aa15a5f8122912c172ddb9dd15b237dc">Genscan</a>, <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT">GeneWise</a> and <a rel="external" href="http://www.nature.com/ng/journal/v25/n2/abs/ng0600_235.html">Exofish</a> predictions with alignments of Tetraodon cDNAs to the genome. This was done automatically using <a rel="external" href="http://genome.cshlp.org/cgi/content/full/12/9/1418">GAZE</a> with a custom-designed configuration and gene structure model.
