Profiles sequence similarity

The aim of the fust dimension breadth is to reveal sequence-function relationships by comparing protein sequences by sequence similarity. Simple bioinformatic algorithms can be used to compare a pair of related proteins or for sequence similarity searches e.g., BLAST (Basic Local Alignment Search Tool). Improved algorithms allow multiple alignments of larger number of proteins and extraction of consensus sequence pattern and sequence profiles or structural templates, which can be related to some functions, see e.g., under http //www. expasy.ch/tools/ similarity. 

Threading techniques try to match a target sequence on a library of known 3D structures by threading the target sequence over the known coordinates. In this manner, threading tries to predict the 3D structure starting from a given protein sequence. It is sometimes successful when comparisons based on sequences or sequence profiles alone fail due to a too low sequence similarity. 

When catalysts are recycled as solid residues, it is important to exclude impurities that may piggyback —such as metal particles—as the active species. This was probed in two ways. First, the tape was removed after a first cycle, rinsed, and transferred to a new vessel. A second charge of 17 and dibutyl ether was added, but not the PhMe2SiH. The sample was warmed to 55 °C, the now off-white tape was fished out , and PhMe2SiH was added. The rate profile was similar to the first cycle (ca. 20% slower at higher conversions), consistent with predominant homogeneous catalysis by desorbed fiuorous species. Second, the second cycle of a sequence was conducted in the presence of elemental mercury, which inhibits catalysis by metal particles [57]. However, the rate profile was the same as a sequence in the absence of mercury. 

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.

Kohring, L.L., Ringelberg, D.B., Devereux, R., Stahl, D.A., Mittelmann, M.M., and White, D.C. (1994) Comparison of phylogenetic relationships based on phospholipids fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria. FEMS Microbiol. Lett. 119, 303-308. 

There are other approaches to family databases that rely more extensively on sequence similarity to define classes of genes or proteins. For example, PROSITE (49) is a resource that uses regular expressions to define patterns of residues that represent biologically significant sequence motifs. Recent versions have incorporated profiles, weight matrices that express the characteristics of a gene... 

Comprehensive transcriptome profiling studies using RNA-Seq (124) have found evidence for many novel exons, and the number of identified alternative splicing forms is much larger than previously expected (137). As alternatively spliced gene structures can be very different from the initial predicted gene structure, current ab initio and sequence similarity methods are not adequate to validate such predictions. Instead, mRNA sequences from RNA-Seq are translated to proteins and used as databases to identify the protein products of these novel exons, even though the final number of sequences that actually become functional proteins in vivo remains unknown (138,139). 

Key Words PSI-BLAST BLAST distant sequence similarity PSSM profile structural relationships. 

MotifSearch uses a set of profiles (representing similarities within a family of sequences) to search a sequence database. 

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