BMC Genomics 2009, 10:490 Additional material Additional file 1 This file contains the accession numbers for all the 19,995 sequences downloaded from Genbank and used in these analyses. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S1.XLS] Additional file 2 This file contains a key to which cDNA accession numbers have been clustered into contiguous sequences using CAP3. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S2.XLS] Additional file 3 This file shows the alignment of sequences that give evidence that Smith-Waterman alignments did not always outperform the normal BLAST algorithm in these tests. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S3.TXT] Additional file 4 BLAST data, though not definitive, gives some evidence for the occur- rence of a genome duplication event in zebrafish. It shows that two zebrafish set genes best match the same human SET gene. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S4.TXT] Additional file 5 Evidence is presented in this file to show that the SRBH method out- performs Homologene for some genes and that phylogenetic analysis does not always assign the correct ortholog. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S5.TXT] Additional file 6 A comparison was made between the SRBH method and Homologene Orthologous group database of the zebrafish to human ortholog assignments by SRBH. 85% of assignments agreed between the two data sources. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S6.XLS] Additional file 7 10 examples were picked at randomly from the Homologene compari- son that did not agree with the RBH results. Results found that in 80% of the cases, the RBH method looked like the correct assignment. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S7.DOC] http://www.biomedcentral.com/1471-2164/10/490 Additional file 8 Data is presented in this file that shows the failed SRBH steps of EST EC394432 ortholog assignment. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S8.TXT] Additional file 9 This file presents further evidence to use a CSRBH as against a SRBH using the carp EST AU052068 as an example. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S9.TXT] Additional file 10 From the 16,665 carp contiguous sequences searched using the Con- ditional Stepped Reciprocal Best Hit (CSRBH) method, 8,726 sequences were successfully assigned a human ortholog. This table dis- plays the ortholog assignments and contains 3,762 non-redundant human genes. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S10.XLS] Additional file 11 From the 4 methods used to predict angiogenesis genes, this table lists the 908 genes that were predicted as angiogenic. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S11.XLS] Additional file 12 This file contains a list of cDNAs that were found to be up-regulated in the Gracey et al. 2004 data set from all three different re-analysis methods. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S12.XLS] Additional file 13 This table contains the 171 predicted cold induced angiogenesis genes. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-490-S13.XLS] Acknowledgements The authors thank Andy Gracey and Andrew Cossins for help with Carp- BASE and the cold carp microarray data; G. Moreno-Hagelsieb for his help and advice with BLAST options; A. F. Karamysheva for advice on angiogenic genes; Estienne Swart for advice on the BLASTO program. John M. J. Her- bert and H. Vorschmitt were funded by Cancer Research UK, project grant no. C4719/A6766. References 1. Hasaneen NA, Zucker S, Lin RZ, Vaday GG, Panettieri RA, Foda HD: Angiogenesis is induced by airway smooth muscle strain. Am J Physiol Lung Cell Mol Physiol 2007, 293(4):L1059-1068. Page 14 of 17 (page number not for citation purposes)