Supplementary files.

All additional files are in Excel format. Footnote to additional files 1-7: Sequences from three libraries were compared by BLASTN to determine which sequences were present in more than one library. The BLASTN cutoff e value was 10^-80. Supplemental tables 1-3 contain the library specific sequences and their annotations, tables 4-6 contain sequences present in HF and HR libraries, or HF and EDIT libraries, or HR and EDIT libraries, and table 7 contains sequences present in all three libraries. The annotations shown are parsed from a BLASTX search of the Arabidopsis protein database ATH1.pep_cm_20040228.

Footnote to additional file 8: The HF, HR and EDIT specific sequences were annotated with Gene Ontogeny descriptors by cross referencing to the best BLASTX hit in ATH1.pep via TAIR [30]. The first three columns of numbers show the number of times a particular GO descriptor was assigned. Most of the assemblies were annotated with multiple GO descriptors so there are more descriptors than assemblies. A total of 5499 GO descriptors were obtained for the HF library, 7222 GO descriptors from the HR and 8381 descriptors from the EDIT library. Pair-wise comparisons were made between each library for the relative proportion of annotations in a particular GO class. For example, 5499 GO annotations were obtained from the HF assemblies; of these, 666 (12.1%) were annotated as "other physiological processes". Similarly, 931 of the 7222 (12.9%) of the GO annotations obtained from the HR library were "other physiological processes". The resultant Chi-squared value is 1.73, suggesting there are not significant differences in the proportion of assemblies annotated as "other physiological processes" between the HF and HR libraries. In contrast, the relative proportion of "other physiological processes" annotations in the EDIT library is 11.8 % (992 out of 7222 total); this is significantly different from the proportions obtained for the HR library (12.9%) but not the HF (12.1%) at p ≤ 0.05. Numbers in the cells are the Chi-squared values calculated. The yellow shaded cells indicate significant p values ≤ 0.05.

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Torres et al. BMC Plant Biology 2005 5:24   doi:10.1186/1471-2229-5-24