Pairwise alignment

Table 2. Percent identities of primary structures from 36 PHA synthases based on pairwise alignments... 

Pairwise Alignment of Prion Sequences (Identity Between Species in %) ... 

The preceding considerations impose serious limitations on simple pairwise alignments that can be overcome in multiple alignments. With sufficient members of a multialignment, both the domain structure and the functionally conserved pattern within that domain context can be discerned. This is true even when the fold of the domain context is indeterminate. 

Finally, as with most pairwise alignment scores (Arratia and Waterman, 1985), the profile-to-sequence match scores need to be normalized as a function of the sequence and the profile s effective lengths. It was noted empirically that the raw scores of profile optimal matches against negative control sequences varied approximately as the logarithm of the sequence length times the profile s information content. The latter is calculated as the mutual information,... 

The fold prediction rate achieved in this analysis is an even greater improvement over the results achieved with pairwise alignment methods (Fischer and Eisenberg, 1997 Gerstein and Levitt, 1997) than reported previously (Wolf et al., 1999). By contrast, several more recent studies that applied PSSM-based methods to protein sets from individual genomes have reported similar prediction rates (Huynen et al., 1998 Paw-... 

Standard sequence similarity search including Peptide Match, Pattern Match, BLAST, FASTA, Pairwise Alignment, and Multiple Alignment... 

Figure 11.2. PIR BLAST Search results for Baltic cod alcohol dehydrogenase. A list of hits (only top 20 hits are shown the EC numbers are deleted from the entries) is followed by pairwise alignments of similar sequences (only the sequence alignment between the query protein and horse liver E isozyme is shown).

To search amino acid sequence against the BLOCKS database at http // www.blocks.fhcrc.org/, select Block Searcher to open the search form. Choose the options, paste the query sequence, and click the Perform Search button. The search returns lists of matched blocks (I.D. descriptions, number of blocks, and combined E values), locations (amino acid positions of individual blocks and its E value), and pairwise alignment of the blocks with the matched query sequences (Figure 12.17). 

Figure 12.17. Search a sequence against Blocks database. The search of cod alcohol dehydrogenase sequence against Blocks database returns a list of hits and pairwise alignments of blocks (only one set is shown).

Figure 6.5. Scoring pairwise alignments. Scoring schemes are comprised of a substitution matrix (S) and gap penalty. Here we consider a pairwise comparison of nucleotide sequences, and the matrix S scores +1 for a match and -1 for a mismatch (left). Three alignments of X and Y are shown, and each is scored using both a linear and an affine gap penalty. The score of each residue pair is shown beneath it, and these are summed to produce the alignment score. Note that the affine gap penalty scores neighboring gaps as -3 and -1 the ordering is not determined, but the end result is their sum -4.

Since PathFinder works in path/distance space, the frame of reference for every molecule is internal and, therefore, no pairwise alignment is necessary when molecules are compared. PathFinder at the same time incorporates information on both overall shape (long distances) and local topology (shorter distances). 

Identity was determined using Pairwise alignment in Homology. Dayhoff mutation matrix, gap penalty and gap length penalty of 6 and 1.65, respectively, were used. 

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