Pair-wise alignment

The VISTA conservation window (for a pair-wise alignment) or several stacked windows (for several pair-wise alignments with the same genome as a base) occupy a central position in the Browser. Conservation is displayed in a standard VISTA format of peaks and valleys (see Note 2), and the height of each peak is indicative of the level of conservation in this area. 

The PIR site also offers facilities for sequence similarity search (BLAST or FASTA), alignment (ClustalW), and analysis (ProClass, ProtFam, RESID, SSEARCH) of proteins. To perform the similarity search, select BLAST or FASTA to open the search form. Paste the query sequence and click the Submit button. The search returns a list of hits with option(s) for modifying the entries (modify query by choosing refine, add to or remove from the list) followed by pair-wise alignment of query sequence versus retrieved sequences (Figure 16.1). The Modify option(s) enable the user to design the list of desired entries. 

The BLAST search of milk lysozyme C (NF00147020) returns a list of hits (with % identity). The list is followed by pair-wise alignment of query sequence versus matched sequences. 

Wang, J. and Feng, J. A. (2005) NdPASA a novel pair-wise protein sequence alignment that incorporates neighbor-dependent amino acid propensities. Proteins 58, 628-637. 

Schmollinger, M., K. Nieselt, M. Kaufmann, and B. Morgenstein. 2004. DIALIGN P Fast pair-wise and multiple sequence alignment using parallel processors. BMC Bioinformatics 5 128. 

This may be trivial if sequence identity between the target sequence and a known 3D stmcture is high (say > 30%), as then simple pair-wise sequence comparison methods (FASTA, SSEARCH ) will easily identify the relation-ship. Where sequence identity is lower and a superfamily or even fold relationship must be identified, recognition of the stmctural similarity between two sequences may be very difficult. Sequence-only methods, such as PSI-BLAST, hidden Markov models and intermediate sequence search, use information from multiple sequence alignments to represent the characteristics shared by related sequences (sequence profiles), and use this to search for stmctural homologues. These profiles can then be augmented by secondary stmcture prediction. ... 

The sequences under smdy must be aligned so that positional homologues may be analyzed. Most methods of sequence alignment are designed for pair-wise comparison. Two approaches to sequence alignments are used, a global alignment (Needleman and... 

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