  Research articleAnnotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFsWalter Salzburger1,2* 1 Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78467 Konstanz, Germany 2 Zoological Institute, University of Basel, 4051, Switzerland 3 Department of Biology, Reed College, Portland, Oregon 97202, USA 4 Guelph Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario N1G 2W1, Canada 5 Physiological Chemistry I, Biozentrum, University of Würzburg, 97074 Würzburg, Germany 6 Section of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
BMC Genomics 2008, 9:96doi:10.1186/1471-2164-9-96
Additional filesAdditional file 1: Gene ontology table (generic GO slim subset for molecular function). Hierarchical classification of the GO slim subset for molecular function. Indented terms are children of parent terms listed above. For each term, the number of A. burtoni assembled sequences that match genes to which Gene Ontology annotations have been assigned at, or below, this general level is given. Note that genes may be assigned to more than one term and child terms may have more than one parent term. For parent terms, the total number of A. burtoni assembled sequences is given in parentheses. Match means that the annotation derives from a gene that was the "best hit" for the A. burtoni sequence at and e-value < 10-12. Format: PDF Size: 36KB Download file This file can be viewed with: Adobe Acrobat Reader Additional file 2: Gene ontology table (generic GO slim subset for biological process). Hierarchical classification of the GO slim subset for biological process. Indented terms are children of parent terms listed above. Genes may be assigned to more than one term. For each term, the number of A. burtoni assembled sequences that match genes to which Gene Ontology annotations have been assigned at, or below, this general level is given. Note that genes may be assigned to more than one term and child terms may have more than one parent term. For parent terms, the total number of A. burtoni assembled sequences is given in parentheses. Match means that the annotation derives from a gene that was the "best hit" for the A. burtoni sequence at and e-value < 10-12. Format: PDF Size: 38KB Download file This file can be viewed with: Adobe Acrobat Reader Additional file 3: Gene ontology table (generic GO slim subset for cellular component). Hierarchical classification of the GO slim subset for cellular component. Indented terms are children of parent terms listed above. Genes may be assigned to more than one term. For each term, the number of A. burtoni assembled sequences that match genes to which Gene Ontology annotations have been assigned at, or below, this general level is given. Note that genes may be assigned to more than one term and child terms may have more than one parent term. For parent terms, the total number of A. burtoni assembled sequences is given in parentheses. Match means that the annotation derives from a gene that was the "best hit" for the A. burtoni sequence at and e-value < 10-12. Format: PDF Size: 34KB Download file This file can be viewed with: Adobe Acrobat Reader Additional file 4: Directed acyclic graph (DAG) of the cichlid specific Gene ontology (GO) slim for molecular function. The graph shows the cichlid specific GO slim for molecular function. Molecular function terms were selected for inclusion in the ontologies such that leaf nodes include approximately 20 annotated genes. Circle size represents relative number of genes annotated to each parent node. Format: JPEG Size: 168KB Download file Additional file 5: Directed acyclic graph (DAG) of the cichlid specific Gene ontology (GO) slim for biological process. The graph shows the cichlid specific GO slim for biological process. Biological process terms were selected for inclusion in the ontologies such that leaf nodes include approximately 20 annotated genes. Circle size represents relative number of genes annotated to each parent node. Format: JPEG Size: 238KB Download file Additional file 6: Directed acyclic graph (DAG) of the cichlid specific Gene ontology (GO) slim for cellular component. The graph shows the cichlid specific GO slim for cellular component. Cellular component terms were selected for inclusion in the ontologies such that leaf nodes include approximately 20 annotated genes. Circle size represents relative number of genes annotated to each parent node. Format: JPEG Size: 134KB Download file Additional file 7: ESTs with higher p-distances. The table shows ESTs where the p-distance between Homo sapiens and haplochromine cichlid amino acid sequences is significantly higher as compared to other fish species (Danio rerio, Takifugu rubripes, Tetraodon nigroviridis and Oncorhynchus mykiss). Annotation means that the Homo sapiens gene was "best hit" for the cichlid sequence (and e-value < 10-50). Format: PDF Size: 70KB Download file This file can be viewed with: Adobe Acrobat Reader Additional file 8: ESTs with smaller p-distances. The table shows ESTs where the p-distance between Homo sapiens and haplochromine cichlid amino acid sequences is significantly smaller as compared to other fish species (Danio rerio, Takifugu rubripes, Tetraodon nigroviridis, and Oncorhynchus mykiss). Annotation means that the Homo sapiens gene was "best hit" for the Cichlid sequence (and e-value < 10-50). Format: PDF Size: 93KB Download file This file can be viewed with: Adobe Acrobat Reader |
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