Thursday, February 29, 2024

BIOINFORMATICS TOOLS

Sequence Analysis Tools

Pairwise Sequence Alignment

  • Needle@EBI – Needleman-Wunsch global sequence alignment tool.
  • BLAST@NCBI – Alignment tool to find regions of similarity between biological sequences.
  • Stucture Alignment – Pairwise structure alignment tool at PDB.
  • Water@EBI –  For local sequence alignment based on Smith-Waterman algorithm.
  • Dotlet@SIB – Sequence comparison with dot plot.

Multiple Sequence Alignment

  • COBALT@NCBI – Constraint-based Multiple Alignment Tool. Computes a multiple protein sequence alignment using conserved domain and local sequence similarity information.
  • Clustal Omega@EBI – Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments.
  • Muscle@EBI – MUltiple Sequence Comparison by Log- Expectation. Multiple sequence comparison with better average accuracy and speed.
  • MAFFT@EBI – Multiple Alignment using Fast Fourier Transform. High speed multiple sequence alignment program.
  • KALIGN@EBI – A fast and accurate multiple sequence alignment algorithm.
  • T-Coffe@EBI – Multiple alignment program that allows to combine results obtained with several alignment methods.
    .
  • STRAP – Intuitive Editor for annotated multiple Sequence and Structure Alignments
  • Weblogo – A web based application designed to easily generate sequence logos .

Sequence Similarity Search

  • NCBI – Sequence similarity seacrh programs at NCBI including PSI-BLAST and PHI-BLAST, etc.
  • EBI  – Sequence similarity search programs at EBI  including FASTA, BLAST and SSEARCH, GGSearch, GLSearch, HMMER. 
  • BLAST/BLAT@Ensembl – Sequence similarity search tool at Ensembl.
  • BLAT@UCSC – Sequence similarity search program available at UCSC genome browser.
  • Sanger BLAST – Sanger Genome Sequencing Projects BLAST.

Primer Design

  • Primer Design – The online primer design tool at BioWeb.
  • Primer Blast – NCBI primer design tool with Blast search.
  • Web Primer – Online primer design tool at the yeast genome database.

Must Read

Meet OncoGPT: Can This Medical Language Model Improve Communication and Support for Cancer Patients?

Meet OncoGPT: Can This Medical Language Model Improve Communication and Support for Cancer Patients?

0
OncoGPT is a customized language model created by Shenzhen Kanghua Juntai Biotech Co. Ltd. researchers in China that is intended to deliver precise medical...
AlphaFLOW and ESMFLOW: A New Approach to Modeling Protein Ensembles with Combined Power of AlphaFold and Flow Matching

AlphaFLOW and ESMFLOW: A New Approach to Modeling Protein Ensembles with Combined Power of...

0
Dynamic structural ensembles play a major role in the biological functions of proteins. For the purpose of learning and sampling the conformational landscapes of...
Unlock the Potential of DeepMod2: A Deep Learning Framework for Precise DNA Methylation Analysis using Oxford Nanopore Sequencing

Unlock the Potential of DeepMod2: A Deep Learning Framework for Precise DNA Methylation Analysis...

0
Reduced representation methylation sequencing for CpG islands or imprinted areas is made possible by Oxford Nanopore sequencing, which offers a distinct advantage over other...
A Team of AI Scientists: Novel Framework for Scientific Discovery from Gene Expression Data

Team of AI-made Scientists: A Groundbreaking System for Automating Scientific Discovery

0
Scientists from the University of Illinois, in collaboration with experts in the field, have unveiled a cutting-edge system named the "Team of AI-made Scientists."...
LLMs in Biomedicine: Navigating the Future with the BioChatter Open-Source Solution

LLMs in Biomedicine: Navigating the Future with the BioChatter Open-Source Solution

0
BioChatter, a new open-source framework developed by Heidelberg University researchers and collaborators, aims to harness the power of large language models (LLMs) for biomedical...