Primers were designed for each sequence (Additional file 11: Table S10) with flanking attL1 and attL2 border sequences to enable recombination with binary plasmids using Gateway® (Invitrogen) for future use in plant transformation assays.
The barcodes have previously been used to split the reads for each lane, create sequence files for each sample and call SNPs for each sample using the MAQ SNP caller (Harismendy et al., unpublished).
For each sample a Sequence file and a Tag file was provided.
Subsequently, a composite-likelihood surface for the recombination parameter is calculated and, for the maximum-composite-likelihood parameter estimates, the maximum likelihood path through the HMM is calculated for each sequence (see Additional file 1).
The script creates a GFF3 file for each sequence in the input scaffold FASTA file and is able to handle both gapped [ e.g., the scaffold (SCF) track] and repeat-masked [ e.g., the repeat-masked (MASK) track] regions in a scaffold.
We carefully checked the concatenated sequences using DNASIS (ver. 3.2; Hitachi Software Engineering) and created a sequence file for each gene.
The numerical frequency of each sequence in the Sequence File for gene expression gives a true indication of relative expression of sequence transcripts.
We show the counts for each sequence pattern in Additional file 2. Regardless of the sequence type, we observed a non-uniform distribution of counts where one base combination had the highest counts of all the base combinations.
The load_sequences.pl program assumes that the sequence definition line, which is preceded by a "greater than sign" for each sequence in a FASTA file, is a Catalog locus ID, and will store that sequence in the MySQL database linked to the Catalog locus.
The formats provided include plain text, XML, RDF and GFF for data files, and FASTA format for sequence files.
