Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices
نویسندگان
چکیده
UNLABELLED Identification of correlated amino acids in proteins has been a topic of broad interest in view of its functional implications and importance in protein design. A new set of pair-to-pair (P2P) substitution matrices for amino acids was recently introduced as a useful tool for inferring information on such correlated sites. We present a website developed for automated application of these matrices for analysis of query sequences. The site offers options for graphical analysis of correlations, as well as visualization of correlated amino acids on representative, structurally characterized, members of the examined family of sequences. AVAILABILITY http://www.ccbb.pitt.edu/p2p.
منابع مشابه
Inconsistent Distances in Substitution Matrices can be Avoided by Properly Handling Hydrophobic Residues
The adequacy of substitution matrices to model evolutionary relationships between amino acid sequences can be numerically evaluated by checking the mathematical property of triangle inequality for all triplets of residues. By converting substitution scores into distances, one can verify that a direct path between two amino acids is shorter than a path passing through a third amino acid in the a...
متن کاملBiol 495s/ Cs 490b/ Math 490b/ Stat 490b
Defining substitution matrices for sequence alignment We need score terms for each aligned residue pair. A biologist with a good intuition for proteins could invent a set of 210 scoring terms for all possible pairs of amino acids, but it is extremely useful to have a guiding theory for what the scores mean. We will derive substitution scores from probabilistic model. Let us establish some notat...
متن کاملAn Evolutionary and Phylogenetic Study of the BMP15 Gene
DNA sequence data contains a wealth of biologically useful information. Recent innovations in DNA sequencing technology have greatly increased our capacity to determine massive amounts of nucleotide sequences. These sequences can be used to specify the characteristics of different regions, interpret the evolutionary relationships between categorized groups, likelihood of performing multiple com...
متن کاملThe (R,S)-symmetric and (R,S)-skew symmetric solutions of the pair of matrix equations A1XB1 = C1 and A2XB2 = C2
Let $Rin textbf{C}^{mtimes m}$ and $Sin textbf{C}^{ntimes n}$ be nontrivial involution matrices; i.e., $R=R^{-1}neq pm~I$ and $S=S^{-1}neq pm~I$. An $mtimes n$ complex matrix $A$ is said to be an $(R, S)$-symmetric ($(R, S)$-skew symmetric) matrix if $RAS =A$ ($ RAS =-A$). The $(R, S)$-symmetric and $(R, S)$-skew symmetric matrices have a number of special properties and widely used in eng...
متن کاملA pair-to-pair amino acids substitution matrix and its applications for protein structure prediction.
We present a new structurally derived pair-to-pair substitution matrix (P2PMAT). This matrix is constructed from a very large amount of integrated high quality multiple sequence alignments (Blocks) and protein structures. It evaluates the likelihoods of all 160,000 pair-to-pair substitutions. P2PMAT matrix implicitly accounts for evolutionary conservation, correlated mutations, and residue-resi...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bioinformatics
دوره 23 14 شماره
صفحات -
تاریخ انتشار 2007