Each 36 bp read was first shortened to 32 bp (a requirement for the alignment tool) and aligned to the grape reference genome [24] using Illumina's ELAND alignment tool.
The Bowtie2 (a.k.a. Bowtie version 2) alignment tool can align reads of very different length.
Consensus sequences were then aligned using MUSCLE alignment tool with default parameters in GENEIOUS PRO.
The trimmed sequences from each barcode bin were aligned using the NAST alignment tool (http://greengenes.lbl.gov) [32].
Finally, we performed a comparison between MP-Align and the SubMAP alignment tool [ 18].
Sequences were aligned using the multiple sequence alignment tool ClustalW [ 38].
Motif-based alignment tool consists of two main parts to align multiple sequences with different affinity scores of STAT TFBSs.
The data were aligned to the reference using the Burrow-Wheeler alignment tool BWA (69, 70).
The remaining sequences are aligned to the full reference genome using a standard alignment tool.
Some cartridges or tone arms come with an alignment tool, but they can be bought separately for $5 to $275.
Our sequence alignment tool StreamAligner resolved these limitations very efficiently.
