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When incorrect alignments are examined independently, the percentage of the boundaries that is overextended increases with identity (Fig. 2B). Figure 2 reports incomplete and overextended alignment boundaries for the 397 123 homologs that were identified by BLASTP and SSEARCH.

Most incomplete alignment boundaries (73% for BLASTP, 76% for SSEARCH) were from alignments in the lowest two identity quartiles.

The positional scores were quantified in the following manner: For each positive PSSM, the alignment boundaries were determined by the overlapping alignments obtained from either Adaptive GDDA-BLAST or rps-BLAST.

The final distribution of all alignment boundaries had 7863 more boundaries within 10 residues of the embedded domain boundary and 3189 additional incomplete boundaries, or 2.5 additional boundaries within ±10 residues for each additional incomplete boundary.

In contrast, incomplete alignment boundaries are more common in low identity alignments, whereas overextended alignment boundaries are more common in high identity alignments.

Different scoring matrices can produce different alignment boundaries.

Alignment boundaries within ±10 residues of the embedded domain boundary are considered correct.

Although most of the alignment boundaries were within 10 residues of the embedded domain boundaries (71% BLASTP, 75% SSEARCH), BLASTP and SSEARCH also created incorrect alignment boundaries.

Looking at all alignments with >36% identity, 16 411 alignment boundaries changed accuracy bins.

The most overextended alignments (>40 residues, Fig. 2) decreased by 2217 alignment boundaries, whereas the most incomplete alignments increased by 399 boundaries.

Results: We measured local alignment start/stop boundary accuracy using a set of queries where the correct alignment boundaries were known, and found that 7% of BLASTP and 8% of SSEARCH alignment boundaries were overextended.