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The BLOSUM62 matrix, the amino acids have been grouped and coloured based on Margaret Dayhoff's classification scheme. Positive and zero values have been highlighted. In bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins.
The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
Alexa-Seq is a pipeline that makes possible to perform gene expression analysis, transcript specific expression analysis, exon junction expression and quantitative alternative analysis. Allows wide alternative expression visualization, statistics and graphs. ARH-seq – identification of differential splicing in RNA-seq data. ASC [56] Ballgown
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 ...
DESeq2 is a software package in the field of bioinformatics and computational biology for the statistical programming language R.It is primarily employed for the analysis of high-throughput RNA sequencing (RNA-seq) data to identify differentially expressed genes between different experimental conditions.
Recently, sequence context-specific amino acid similarities have been derived that do not need substitution matrices but that rely on a library of sequence contexts instead. Using this idea, a context-specific extension of the popular BLAST program has been demonstrated to achieve a twofold sensitivity improvement for remotely related sequences ...
Amino acid replacement is a change from one amino acid to a different amino acid in a protein due to point mutation in the corresponding DNA sequence. It is caused by nonsynonymous missense mutation which changes the codon sequence to code other amino acid instead of the original.
Fold change is a measure describing how much a quantity changes between an original and a subsequent measurement. It is defined as the ratio between the two quantities; for quantities A and B the fold change of B with respect to A is B/A.