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
Enhancing Drug Discovery with NRGSuite-Qt: A PyMOL Plugin for Virtual Screening and Docking
Drug discovery and protein engineering are some of the most challenging aspects of cutting-edge scientific research. It is also a field that holds great...
Visualizing Omics Data Made Easy with DataColor’s 600+ Parameters
The display of many types of data with different orders of magnitude is a critical challenge in the rapid development of high-throughput omics technologies....
From Complexity to Simplicity: BATCHIE’s Role in Uncovering Cancer Drug Synergies
Combination therapies have emerged as a new strategy in the battle against cancer and are viewed as superior to previously existing treatment options. There...
IRB Barcelona Unveils Oncodrive3D to Identify Cancer Driver Genes Using 3D Protein Structures
Finding the genes that can cause tumors in various tissues is one of the main objectives of cancer genomics. Computational techniques that use various...
Top 30 Python Libraries Used in Bioinformatics
Bioinformatics sits at the fascinating intersection of biology, computer science, and data analysis, with Python as a powerful language that drives groundbreaking research and...