MOTIVATION: A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools. RESULTS: We describe COBALT, a constraint based alignment tool that im...
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 ...
RNA-Seq quality was assessed using FastQC. Adapter sequences and low quality bases were trimmed using Trimmomatic46. Sequence alignment was performed using STAR47against the CHO genome (GCF_000419365.1_C_griseus_v1.0) with the default parameters. The expression of each gene was quantified using HT...
Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec a
A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools. We describe COBALT, a constraint based alignment tool that implements a general ...
sequence alignment (MSA). After describing some general ideas that relate MSA and consensus sequences and presenting a statistical thermodynamic framework that relates consensus and non-consensus sequences to stability, we detail the process of designing a consensus sequence and survey reports of ...
as the resulting epitope will most likely be a linear sequence. Basic Local Alignment Search Tool (BLAST) searches extensive sequence databases for regions with high sequence similarity to an input sequence [89]. This tool is therefore ideally suited to identify regions in the proteome that are ...
The protein sequences of Epd were extracted from the BRENDA database based on EC number 1.2.1.72. Multiple sequence alignment and comparative analysis of the protein were conducted using the command-line version ClustalW2105. Phylogenetic trees were constructed using the data from the alignments in...
Protein sequence design is critically important for protein engineering. Despite recent advancements in deep learning-based methods, achieving accurate and robust sequence design remains a challenge. Here we present CarbonDesign, an approach that draws inspiration from successful ingredients of AlphaFold and...
CRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis and visualization of the resulting datasets,