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In terms of coverage, only 1% of the total number of compositionally homogeneous domains could be considered "isochores" which covered less than 20% of the genome. [ 35 ] Since its inception the theory received wide attention and was extensively used to explain findings emerging from over dozen new genome sequencing studies.
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
The pioneering approaches for sequence analysis were based on sequence alignment either global or local, pairwise or multiple sequence alignment. [3] [4] Alignment-based approaches generally give excellent results when the sequences under study are closely related and can be reliably aligned, but when the sequences are divergent, a reliable ...
In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome, transcriptome or proteome of an organism, and can also involve only selected segments or regions ...
An isochromosome is an unbalanced structural abnormality in which the arms of the chromosome are mirror images of each other. [1] The chromosome consists of two copies of either the long (q) arm or the short (p) arm because isochromosome formation is equivalent to a simultaneous duplication and deletion of genetic material .
For example, the restriction enzymes HpaII and MspI are isoschizomers, as they both recognize the sequence 5'-CCGG-3' when it is unmethylated. But when the second C of the sequence is methylated, only MspI can recognize it while HpaII cannot. An enzyme that recognizes the same sequence but cuts it differently is a neoschizomer. Neoschizomers ...
Sequence clustering is often used to make a non-redundant set of representative sequences. Sequence clusters are often synonymous with (but not identical to) protein families. Determining a representative tertiary structure for each sequence cluster is the aim of many structural genomics initiatives.
The ancestral sequence of sequence 1 can be reconstructed from B and C, as long as at least one outgroup is available, e.g. D or E. For example, sequences B and C are different in position 4, but since sequences D and E have a C in that position, sequence 1 most likely had a C as well.