After excluding probes that had consistently low expression across all samples (see Methods) and annotating probes based on the POParray database [ 25], we obtained expression data for 41 probes corresponding to 48 BAHD genes (some probe sequences match multiple gene targets, and some gene targets are represented by multiple probes).
The functional modules were identified by using SCAN, a fast structural clustering method, and annotated with KEGG pathways.
In the supplementary material (File S2 sheet 'correlation Analysis'), the correlation of each of the 1,372 probes that were selected by our method is given (and annotated, including Affymetrix and Stanford's Source outputs) to facilitate further analyses.
Densities of polymorphisms were estimated for 23,717 genes whose functions are clearly defined or suggested (similarity category I III, see Materials and Methods) and genes annotated as conserved hypothetical proteins (similarity category IV).
Through automated and manual methods, we have identified and annotated large numbers of splicing variations in Arabidopsis.
These BAC sequences were assembled and annotated (see Methods, Additional files 2 and 3: Tables S1 and S2), revealing a total of 153 genes, 78 of which are from S. vulgaris.
The sequence was assembled and annotated as described in Methods.
The methods for editing and annotating Darwin's manuscripts are intended to produce transcriptions whose content is equal in value to the manuscripts from which they are derived.
We applied the MemO pipeline [ 36], which reports the consensus prediction among several methods, to identify and annotate transmembrane proteins in our various datasets, and used PPIs involving a predicted transmembrane protein as input into our four variant approaches.
Furthermore, glbase incorporates methods to overlap and annotate genomic intervals (similar to BEDTools [ 2]), to map common values across two lists (similar to but more powerful than the UNIX command 'join'), support for genomic coordinates to gene annotations and for extracting sequence data from FASTA files.
Because the two genomes were sequenced and annotated several years apart using different methods, we re-annotated both genomes, making several types of corrections in order to assure that comparisons between the two were valid.
