Closely related sequences

Here, two different sequences from transth3Tetin were successfully combined into mixed fibrils [54], This is not always the case, however. For amyloidogenic proteins, the ability of other fibrils to act as cross-seeds for growth is known to depend on sequence similarity [55]. Seeding hen lysozyme solutions with seeds formed from closely related sequences (e.g. hen and other lysozymes) led to the largest increases in the rate of formation of fibrils. Consequently, there may be some restrictions on the selection of distinct peptide sequences to produce scaffolds. 

A potential source of inaccuracy in the MDM model comes from the extrapolation of alignments of closely related sequences to model distant relationships. For example, closely related sequences are dominated by... 

A sophisticated model of protein evolution was developed by Dayhoff et al. (1978) who measured the frequency with which each amino acid was replaced by every other in sets of closely related sequences. This was converted into a Markov model, which was used to generate the probability of any amino acid being substituted by any other or remaining unchanged after different amounts of evolution. The amount of evolution was measured in PAMs (point accepted mutations), which are mean numbers of substitutions per 100 residues. This is, of course, the same... 

The options above represent mutations in the DNA with base changes indicated in boldface type. For each mutation described in the questions below, choose the most closely related sequence change in the options above. 

Several derivatives of 4,5,6,7-tetrahydrobenzo[c]thiophen-4-one (Table III) have been prepared by the sequence of reactions exemplified by Eq. (2) or by a closely related sequence of reactions. When... 

Fig. 2.5. A quasi-species-type mutant distribution around a master sequence. The quasi-species is an ordered distribution of polynucleotide sequences (RNA or DNA) in sequence space. A fittest genotype or master sequence /m, which is commonly present at highest frequency, is surrounded in sequence space by a cloud of closely related sequences. Relatedness of sequences is expressed (in terms of error classes) by the number of mutations which are required to produce them as mutants of the master sequence. In case of point mutations the distance between sequences is the Hamming distance. In precise terms, the quasi-species is defined as the stable stationary solution of Eq. (2) [16,19, 20], In reality, such a stationary solution exists only if the error rate of replication lies below a maximal value called the error threshold. In this region, i.e. below...

Two minor processes sometimes operate competitively with that illustrated in the scheme. One of these involves 1,4-addition of the second vinyl anion to give a reactive intermediate that differs structurally from 1, but is capable of setting into motion a closely related sequence of chemical events leading to an isomeric diquinane.4 This is the route followed to produce the minor product characterized here. The other option consists of cis-t, 2-addition, an event that is followed by a dianionic oxy-Cope rearrangement via a boat-like transition state.4 When sufficient substitution is present to allow the installation of multiple stereogenic centers, the adoption of this pathway is easily distinguished from the electrocyclic alternative since a cis relationship between relevant substituents is in place, instead of the trans arrangement required by the electrocyclization cascade. 

The advent of quantitative PCR techniques makes it possible to quantify the abundance and expression of a specific gene and closely related sequences, or the abundances of taxonomic groups depending on the specificity of quantitative PCR... 

This technique was also used to monitor the effects of applied electric fields on hybridization and dchybridization not surprisingly, it was found that even small fields can significantly accelerate these processes. Mismatched sequences were particularly susceptible to potential-induced dehybridization, an effect that is potentially useful in discriminating between closely related sequences. As similar electric fields are involved in electrochemical assays, the effects of these fields on the DNA-film structure must be considered in the design and interpretation of DNA detection experiments. 

Generation of on-the-fly comparisons can be carried out between up to five sequences, using a choice of BLASTZ, MUMmer, or National Center for Biotechnology Information BLAST. A series of preconfigured settings are available tailored to specific kinds of queries, i.e., sequences less than 1 Mb or closely related sequences, however the application also allows full access to the available parameters of each program, enabling experienced users to customize comparison parameters. 

Ovcharenko, I., Boffelli, D., and Loots, G. G. (2004) eShadow a tool for comparing closely related sequences. Genome Res. 14, 1191-1198. 

---