They are shown in Figure 9, as they appear after successful alignment, with different colors associated to each range scan (naturally high color mixing due to scan interpenetration is present).
These blast results identified possible frame shifts and intron inclusions because they appear as multiple alignments in the Blast output.
These alignments are kept as they appeared in the final release of Pfam before they were withdrawn (Table 1).
Most alignment failures appear to be the result of chimeric inserts.
However, in one alignment, codons are conserved (same codons occur in the same column), while in the other alignment codons appear only once in a column.
Interestingly, the alignment programs appear to have a stronger effect on sensitivity, whereas the variant calling programs appeared to effect specificity more strongly.
Therefore, by identifying positions within a multiple sequence alignment which appear to coevolve, it is possible to infer that these positions are in close proximity in the native protein structure.
Even gestures designed to bring Wartburg and Venusberg in closer alignment appear trite.
The pipeline we proposed in Section "Pairwise alignment technique" may appear to be constituted by independent blocks, thus easily interchangeable with alternative ones.
These can be displayed and analysed starting from the BLAT output page and clicking on "details", so that the sequences of each block and their alignment appear.
