Proteomics sequence similarities

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.

Software tools for database searching and available protein sequence databases for protein identification were reviewed [130-131], Liska and Shevchenko [132] reviewed approaches to study proteomes with nonsequenced genomes via sequence similarity database searching. 

Han L, Cui J, Lin H et al. Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity. Proteomics 2006 6 14) 4023-4037. 

The translation of the peptide sequence to functions in a protein molecule can be expressed as modular units (motifs and domains) that confer similar properties or functions in a variety of proteins. Based on characteristics of modular units, proteomes can be classified into families of proteins possessing related functions. For instance, some proteins play a key role in intercellular signaling pathways and some are structural, while others participate in metabolism. Up to 40% of proteins are encoded by the genome and carry out unknown functions, which still need to be discovered. 

S-L-x(i i5)-R-(N/F/xF) or M-L-R-(S/N)-F, picked out 138 sequences with 67% showing similarity to known proteins involved in metabolic pathways, electron transport, protein import, protein folding and oxygen scavenging pathways (Carlton et al. 2007). There are undoubtedly variations on these consensus, as have been found during proteomic studies (our unpublished data). 

The current situation in bioinformatics is characterized by an avalanche of DNA sequences from the human genome project and similar programs and, consequently, an exponential increase in DNA sequences but only a linear increase in protein 3D structures. While multitudes of putative genes have been annotated, up to 90% of all known DNA sequences have no assigned, i.e., experimentally proven, function. From this situation arise the need for interpretation of DNA sequences by information technology, and moreover, analysis of functional genomics and proteomics (see Chapter 15). 

Proteomics is concerned with the analysis of the complete protein complements of genomes. Thus proteomics includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, activities, and functions. This chapter focuses on protein sequences as the sources of biochemical information. Protein sequence databases are surveyed. Similarity search and sequence alignments using the Internet resources are described. 

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