In the read 2 example, a shift permitted the addition of one deletion at the beginning of the alignment.
If the contaminant is found within the read (C), the bases from the 5′ end of the read to the beginning of the alignment are retained.
Each protein gene was inferred to begin at an eligible initiation codon nearest to the beginning of its alignment with homologous genes that does not cause overlap with the preceding gene.
Each protein gene start was inferred as the eligible initiation codon nearest to the beginning of its alignment with homologous genes that does not cause overlap with the preceding gene.
The beginning of the alignments for the genes COX1, CYTB, ND1 and ND6 were slightly adjusted.
For the beginning of the CDS, alignment of the nucleotide sequences was guided by the amino acid sequence alignment [ 62].
Then, the Met (putative translation start) codon closest to the beginning of the BLAST alignment is found and declared to be the gene start predicted by BLAST.
The algorithm is easily modified for local alignment of read patterns by including the beginning of a new local alignment (with score 0) in the recursion (6), analogous to the Smith Waterman sequence alignment algorithm.
For instance, the beginning of the T. pretoriensis CBS5080 (alignment positions 169−245 in Figure S1) was identical with T. delbrueckii CBS5448, but differed from either K. thermotolerans or L. mirantina by at least 12 nucleotides plus one indel.
Overtime, I began to realize that I was out of alignment.
