Sequence alignment tools

CLUSTALW is a sequence alignment tool, which takes as input a set of sequences and produces a multiple alignment of those sequences. 

Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. and Higgins, D. G. The CLUSTAL X windows interface flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 4876-4882, 1997. 

Galtier, N., Gouy, M., and Gautier, C. (1996). SEAVIEW and PHYLO WIN two graphic tools for sequence alignment and molecular phylogeny. Comp. Appl. Biosci. 12, 543-548. 

The ExPASy server (www.expasy.chl is one of the most useful servers, where almost any bioinforma tic tool can be found, together with useful links to other websites such as NCBI or EBI. The several access databases are descriptive, easy to follow, and up to date. Protein data bank searches with SwissProt or Trembl, as well as sequence alignments using either SimAlign (for two sequences) or ClustalW (for more than two protein sequences) can be started from ExPASy, to name just a few of the possibilities available. Access is also given to the Roche Applied Science Biochemical pathways where either keyword searches for particular enzymes or for metabolites can be performed, or entire metabolic pathways or sections thereof can be visualized. Proteomics evaluation is also available on ExPASy, which features free 2D-PAGE software called Melanie. 

The site mainly offers useful software for sequence alignment such as ALIGN. It also offers some other useful tools such as PRINTS (Protein motif fingerprint data) and MAXD for microarray data storage and analysis. 

A sequence alignment is a way of determining the similarity between two strings. This is a classical question in computer science, and has an exact solution referred to as the Smith/Waterman alignment. Unfortunately, this exact solution can be slow when analyzing large sequences, and therefore, approximate methods, such as Basic Local Alignment Search Tool (BLAST), have been developed to identify very similar sequences. 

Naive approaches avoid theoretical assumptions and instead focus on statistics about solved RNA structures, using these to probabilistically align new sequences with solved structures. One elegant approach to this problem has used an rRNA database to generate a novel RNA-specific substitution matrix. The advantage of this approach is that it makes the whole spectrum of primary-structure sequence-analysis tools available for secondary-structure prediction (27). 

Sequence assembly tools The iterative sequence alignment by incorporating the matched consensus sequence from the previous search into the subsequent round of search is called sequence assembly. The available tools are Staden assembler, TIGR assembler, and so on. 

Figure 11,4. ExPASy Proteomic tools. ExPASy server provides various tools for proteomic analysis which can be accessed from ExPASy Proteomic tools. These tools (locals or hyperlinks) include Protein identification and characterization, Translation from DNA sequences to protein sequences. Similarity searches, Pattern and profile searches, Post-translational modification prediction, Primary structure analysis, Secondary structure prediction, Tertiary structure inference, Transmembrane region detection, and Sequence alignment.

Figure 11.6. Amino acid sequence alignment at EBI. Amino acid sequences of type C lysozyme are submitted to ClustalW tool of EBI, and the alignment is retrieved from the notified URL...

Select the Generate Structural Alignment tool of the Fit menu to initiate the sequence alignment which can be viewed by clicking the little text icon. 

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