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.
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  • 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.

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