Saturday, December 10, 2022

BIOINFORMATICS TOOLS

Proteomics Tools

Protein Sequence Analysis and Function Prediction

  • ProtParam – Allows the computation of various physical and chemical parameters for a given protein sequence.
  • PEAKS CMD – It can perform de novo sequencing, protein identification, multi-engine protein identification,
    PTM search, sequence homology searching and quantification.
  • PEAKS Studio Xpro – A software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post-translational modifications (PTMs) and sequence variants (mutations), and peptide/protein de novo sequencing. (Commercial)

  • PANTHER-PSEP – Estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein.
  • ProtScale – It can compute and represent the profile produced by any amino acid scale on a selected protein.
  • PredictProtein – Service for protein structure prediction, protein sequence analysis, protein function prediction, protein sequence alignments, bioinformatics.
  • MutationTaster – Identifies disease-causing ability of sequence alterations.
  • MuPIT Interactive – Mapping variant positions to annotated, interactive 3D structures.

  • LS-SNP – An annotated database of SNPs. Currently only coding non-synonomous SNPs found in human genes are included. 

  • PeCop – Predicting Persistently Conserved Positions.

Protein Domain Prediction

  • SMART@EMBL – The web server is used for the identification and analysis of protein domains within protein sequences..
  • MEME – Motif-based sequence analysis tools.
  • InterPro@EBI – Protein domain and family classification database.
  • TMHMM 2.0 –  Web server for the prediction of transmembrane helices in proteins.

Must Read

Overview of the full workflow and tools performed by TransFlow (Transmission Workflow).

TransFlow: a Fast and Efficient Snakemake Workflow for Whole Genome Sequencing Based Transmission Analysis...

0
TransFlow (Transmission Workflow), a convenient, quick, effective, and thorough WGS-based transmission analysis pipeline, is presented by Chinese researchers. TransFlow integrates a number of cutting-edge...
Federated Machine Learning Powers the Biggest Brain Tumor Study to Date while Protecting Patient's Data

Federated Machine Learning Powers the Biggest Brain Tumor Study to Date while Protecting Patient’s...

0
Federated machine learning enables the largest brain tumor study ever conducted without sharing patient data by allowing researchers to securely analyze distributed datasets while...
MIT Researchers Used Large Language Models to Decode Electronic Health Records.

MIT Researchers Used Large Language Models to Decode Clinical Health Records in Few Shots

0
Researchers from MIT CSAIL employed a potent deep-learning model to extract crucial information from electronic health records that might help with personalized medicine. The adoption...
Hidden Patterns Involved In Patients With Multimorbidities

UCL Researchers Unraveled the Hidden Patterns Involved in Patients with Multimorbidities

0
Researchers at University College London discovered multimorbidity and comorbidity illness trends using a dataset spanning 3.8 million patients in England. Patients and clinicians can...
A multi omics approach to earth's microbiomes project

A Multi-Omics Approach to Earth’s Microbiomes Project Demonstrates Microbial and Metabolite Diversity

0
Contrasting sharply with the little knowledge of the microbial world's underlying structure is the rising awareness of its significance and variety. Despite recent developments...