Open Access Research article

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

David A Fitzpatrick1,2*, Peadar O'Gaora3, Kevin P Byrne4 and Geraldine Butler1*

1 UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

2 Department of Biology, The National University of Ireland, Maynooth, County Kildare, Ireland

3 UCD School of Medicine and Medical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

4 Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Ireland

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BMC Genomics 2010, 11:290 doi:10.1186/1471-2164-11-290

Published: 10 May 2010

Additional files

Additional file 1:

Merging partial open reading frames. Section of alignment illustrating that the original automatically called gene sets contained partial open reading frames. In this example LELG_01496 and LELG_01495 from L. elongisporus are merged to give a new single gene (LELG_01496*).

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Additional file 2:

List of partial ORFs in datasets obtained from sequencing centers. Merged genes all have a * suffix and are present in CGOB. Partial ORFs have been removed from CGOB pillars but are present in the CGOB Blast database.

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Additional file 3:

List of all tandem duplicates located by CGOB. a) Clusters are labeled 1-502. Those with a dN/dS value > 1 are highlighted in red. Clusters displaying a ^ indicate that the initial BLAST search strategy failed to infer homology. Clusters displaying * indicate that there are intervening genes but they may be spurious gene models. Clusters displaying (INS) indicate that there is one intervening gene. b) List of tandem clusters with a dN/dS > 1.

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Additional file 4:

List of CGD pathways and the corresponding genes that display evidence of clustering in each Candida species. Numbers in parenthesis refer to cluster numbers and are retained across species. Clusters with "sig" in parenthesis infer that the cluster is significantly better than randomized data.

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Additional file 5:

List of KEGG pathways and the corresponding genes that display evidence of clustering in each Candida species. Clusters have been assigned numbers (KC) so it is possible to locate a cluster present in one species that is absent in another. Clusters denoted with a TD infer that the cluster has arisen through tandem duplication. Clusters that are significantly better than randomized data are highlighted with purple shading.

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Open Data