Although we show results here using a reference sequence, this method, as the others, can be applied without a reference.
Using a reference sequence and comparing it with the query sequence, only the differences (i.e., variants) between the two are encoded into a VCF file.
For these reasons at that time it was required to use a reference sequence coming from the assembly of multiple genomes.
Exon/intron boundaries were identified using a reference sequence from A. burtoni (DQ386648) and checked by homology comparison with reference sequences from pufferfish (U63926), zebrafish (AF240639) and trout (AJ417832).
For the pooled exome sample, the alignment was performed using Novoalign using a reference sequence for the 165,637 bait intervals from the exome capture plus 76 bp flanking bases.
Retained duplicate transcripts corresponding to isoflavone synthase/cellulose synthase, galactinol synthase, raffinose synthase and caffeoyl-CoA o-methyltransferase were identified with TBLASTX (default parameters) using a reference sequence against all soybean ESTs [ 58].
The breseq pipeline uses a reference-sequence-based mapping strategy, which includes evaluating new sequence junctions supported by split-read alignments and tracking multiply-mapped reads, to predict point mutations and structural mutations from short-read DNA resequencing data.
These A. marginale sequencing reads were then used for a second Megablast alignment using as a reference sequence 28 nucleotides from the Himar1 terminal inverted repeats (TIR).
The consensus sequence from each of these contigs was used as a reference sequence to which individual sequence reads were aligned using PCAP.
This uses a reference set of sequences to train a model and then utilizes that model to predict coding regions in the genome of interest.
One is used as a reference sequence, and the other is shifted relative to the reference.
