This chapter is the longest in the book as it deals with both general principles and practical aspects of sequence and, to a lesser degree, structure analysis. Although these methods are not, in themselves, part of genomics, no reasonable genome analysis and annotation would be possible without understanding how these methods work and having some practical experience with their use.
To exert their biological functions, proteins fold into one or more specific conformations, dictated by complex and reversible non-covalent interactions. Determining the structure of a protein can be achieved by technics such as crystallography, nuclear-magnetic resonance spectroscopy, and dual polarization interferometry, and has implication for their biological functions.
The programs developed for sequence analysis deal with, database searching, sequence comparison, multiple sequence alignment, protein analysis, enzyme mapping, evolutionary analysis, pattern searching, motif searching, and 3-D visualization3. Sequence analysis programs are not limited to those tools, they are just the main analysis tools.
Bacterial protein expression systems are popular because bacteria are easy to culture, grow fast and produce high yields of recombinant protein. However, multi-domain eukaryotic proteins expressed in bacteria often are non-functional because the cells are not equipped to accomplish the required post-translational modifications or molecular folding.
Please use one of the following formats to cite this article in your essay, paper or report: APA. Aliouche, Hidaya. (2019, January 07). Computational-based Approaches to Protein Function Prediction.
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Evaluates the accuracy of protein sequence alignment methods. CASA is an implementation of the alignment accuracy benchmark. The server produces graphical and tabular comparisons of the accuracy of a user’s input sequence alignments with other commonly used programs, such as BLAST, PSI-BLAST, Clustal W, and SAM-T99. The website provides the sequences to be aligned and several lists of.
ProfileScan uses the method of Gribskov et al. (CABIOS 4(1); 61-66 (1988)) to find structural and sequence motifs in protein sequences. These motifs are represented as profiles in a library. Because more than one alignment between a sequence and a particular motif can be found, each repeat of a duplicated structure (such as the zinc finger motif) can be presented.