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Last Annotation of Fugu rubripes at JGI

2005

Salamov, Asaf;
Terry, Astrid;
Putnam, Nicholas;
Rokhsar, Dan;
Grigoriev, Igor;
Loh Eddie;
Venkatesh, Burappa
et al.

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Last annotation of Fugu rubripes at JGI
Phylogeny of eukaryotes (Baldauf, Science, 2003)
Outline of the Assembly Process: JAZZ, the JGI In-House Assembler
Fugu Assembly Statistics
Methods used for fugu annotation at JGI
Fraction of conserved sequence in Fugu relative to Tetraodon and Zebrafish (according to Vista)
KOG/GO/KEGG
Summary of JGI annotations for Fugu v.4
Comparison between JGI4 and Singapore4 annotations
Pfam domain comparison between different annotations
NJ-tree (Phylip) based on Pfam domain content distances
Detection of possibly ‘missed’ genes based on Pfam domain profile
76 domains are absent in tetraodon (TN), but present in human(HS), fugu (FR) and ciona (CI)
156 domains are absent in zebrafish (DR), but present in human(HS), fugu (FR) and ciona (CI)
Acknowledgements

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Pathway Evolution Through a Bottlenecking-Debottlenecking Strategy and Machine Learning-Aided Flux Balancing.

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