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
Unlocking Cellular Mysteries with CellReasoner: A New AI Tool for Biologists
In the rapidly evolving field of single-cell biology, accurately identifying cell types from complex datasets remains a cornerstone of research. A team of scientists...
Minimal Data, Maximal Impact: The Future of Peptide Design with MDMI
Peptides, which are short chains of amino acids, have become increasingly important in the world of medicine and biotechnology. Their unique properties make them...
Can Machine Learning Finally Crack the Protein Expression Code?
A team of researchers from the University of Edinburgh and collaborators from institutions like Stanford and UC San Francisco have tackled a central question...
AlphaGenome: DeepMind’s New AI Model for Unlocking Genome Function
Imagine holding a book written in a language where only 2% of the pages contain clear instructions, while the remaining 98% seem like indecipherable...
From Boltz-1 to Boltz-2: Did We Finally Bridge the Gap Between Structure and Affinity?
In modern biology, accurately simulating biomolecular interactions is a major difficulty. Our capacity to predict biomolecular complex structures has significantly improved with recent developments...