While sequence alignments are accurate for proteins of high sequence similarity, they become unreliable as they approach the so-called 'twilight zone' where sequence similarity gets indistinguishable from random. For such distant pairs, structure alignment is of much better quality. Nevertheless, ...
Protein sequence alignment is a key component of most bioinformatics pipelines to study the structures and functions of proteins. Aligning highly divergent sequences remains, however, a difficult task that current algorithms often fail to perform accurat
pairwise sequence alignmentsearch algorithmssequence databasesword methodGiven a set of biological sequences, it is often a desire to identify the similarities shared between the sequences. This information will give further data about the functionality, originality, or the evolution of the species ...
We propose a Bayesian method to align proteins usingboth the sequence and 3-D structure of the proteins. The problem involves whatare known as "gaps" in the sequence, which we incorporate in our model, and anMCMC implementation is provided. Also, we show that the procedure can be usedto ...
An MSA is a matrix\({{{\mathcal{M}}}\)withLcolumns, representing the different amino-acid sites, andMrows. Each rowi, denoted byx(i), represents one sequence of the alignment. We will refer toLas the MSA length, and toMas its depth. For all but one (PF13354) of our full MSAs,...
5) Function to Sequence CNN-based • VAE-based • GAN-based • Transformer-based • Bayesian method • Reinforcement Learning • Flow-based • RNN-based • LSTM-based • Autoregressive • Boltzmann machine • Diffusion-based • GNN-based • Score-based 6) Function to ...
Kumar and Gromiha (2006)developed theProtein-protein InteractionsThermodynamic Database (PINT), which contains several thermodynamic parameters along with sequence and structural information, experimental conditions, and literature information. Each entry contains numerical data for thefree energychange,dissociat...
Althaus E, Caprara A, Lenhof HP, Reinert K (2002) Multiple sequence alignment with arbitrary gap costs: computing an optimal solution using polyhedral combinatorics. Bioinformatics 18(Suppl 2):S4–S16 Article PubMed Google Scholar Altschul SF (1996) Local alignment statistics. Meth Enzymol 274...
retrieve multiple sequence alignment results as well as various statistics on the contact map, and compare to other RR contact prediction methods by uploading comparison maps. Contact Maps can be shown in either binary or in continuous formats, the former indicating just the presence/absence of cont...
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9, 173–175 (2012). Article Google Scholar Johnson, L. S., Eddy, S. R. & Portugaly, E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinform. 11, 431 (2010)...