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Sequence comparisons

Homology searches

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Hidden Markov models

Hydrophobicity analyses

Topology and helix packing

Protein localization

Secondary structure

Super-secondary structure

3D structure

 

    Sequence comparisons in the internet:

    Dot matrices

  • Examples of DotPlot Visualization Technique
  • DotPlot @ Univ. Düsseldorf, Germany
  • DotPlot: Dot matrix comparison of two sequences (not for Macintosh browser!)

    Classic algorithms

  • Needleman & Wunsch at EBI: Global alignment
  • Smith & Waterman at EBI: Local alignment

    Pairwise sequence comparisons

  • BCM: Pairwise sequence comparisons: SIM, (ALIGN/LALIGN), BLAST2, LAP2, PGWISE, PCWISE
  • ExPASy: Sequence comparisons: SIM, LALIGN (see below), Dotlet
  • Sequence analysis Tools at EBI
    • EMBOSS Pairwise Alignment Algorithms (global and local)
    • Wise2 (basic) compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors
    • Wise2 (advanced)
    • Wise2 Dna Block Aligner aligns two sequences under the assumption that the sequences share a number of colinear blocks of conservation separated by potentially large and varied lengths of DNA in the two sequences
    • Wise2 PromoterWise compares two DNA sequences allowing for inversions and translocations, ideal for promoters

  • ALIGN at Genestream
  • BLAST 2 at NIH: Comparison of two sequence
  • BLAST 2 at Genestream
  • GLASS at MIT: GLobal Alignment SyStem
  • LALIGN at EMBnet: Finds multiple matching subsegments in two sequences (SIM-based code)
  • LALIGN at Genestream
  • LFASTA at PBIL: Local Alignment Tool for Nucleic Sequences
  • Palign (Stockholm): Protein alignment
  • SIM at SIB/ExPASy: Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW
  • SIM4 at PBIL: Program to align cDNA and genomic DNA
  • ToPlign (Toolbox for Protein ALignment) at Fraunhofer: Pairwise and multiple sequence comparison
    • ToPlign: Login at BioSolveIT (OUTDATED)

  • PRSS3 at EMBnet: evaluates the significance of a protein sequence alignment

    Multiple sequence comparisons

  • BCM: Multiple sequence comparisons: ClustalW, CAP, MAP, PIMA, MSA, BLOCK MAKER, MEME, Match-Box
  • ExPASy: Sequence comparisons: ClustalW, KALIGN, MAFFT, Muscle, T-Coffee, MSA, DIALGN, Match-Box, Multalin, MUSCA (see below)

  • ClustalW at EBI
  • ClustalW at PBIL
  • ClustalW at MyHits/SIB
  • ClustalW at EMBnet

  • COBALT at NIH: Multiple alignment incorporating pairwise constraints
  • Coffee's at CNRS Marseille
  • Coffee's at EBI
  • Coffee's at SIB
  • T-Coffee at BioAssist Wageningen
  • DIALIGN at Bielefeld University: Multiple sequence alignment based on segment-to-segment comparison
  • Kalign at EBI: A fast and accurate multiple sequence alignment algorithm
  • Kalign at Karolinska
  • MAFFT at EBI: Multiple Alignment using Fast Fourier Transform
  • MAFFT at MyHits/SIB
  • MAFFT at Kyushu University
  • Match-Box at University of Namur (only proteins!)
  • MSA at Genestream: Multiple Sequence Alignment
  • Multalin at INRA
  • Multalin at PBIL (only proteins!)
  • MUSCA at IBM: Multiple sequence alignment using pattern discovery (only proteins!)
  • MUSCLE at Drive5: MUltiple Sequence Comparison by Log-Expectation
  • MUSCLE at EBI
  • MUSCLE at BioAssist Wageningen
  • PRALINE: PRofile ALIgNEment, at Vrije Universiteit Amsterdam
  • PROBCONS: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences, at Stanford University

  • SAGA: Sequence Alignment by Genetic Algorithm (software for download)
  • SATCHMO at Drive5: Simultaneous Alignment and Tree Construction using Hidden Markov mOdels (software for download)
  • SSMAL at DKFZ: Shuffled Similarities with Multiple ALignments (software for download) (OUTDATED)

    Profile comparisons

  • COACH at Drive5: COmparison of Alignments by Constructing HMMs (software for download)
  • COMPASS at University of Texas: COmparison of Multiple Protein Alignments with Assessment of Statistical Significance
  • FFAS03: Fold and Function Assignment System
    Genome comparisons:

  • TaxPlot
  • GRAPe at University of Oxford: Probabilistic whole-genome re-alignment (for download)
    Similarity matrices:

  • PAM250: Percent Accepted Mutation-Matrix (Dayhoff et al., 1978)
  • BLOSUM62: Blocks Substitution-Matrix (Henikoff and Henikoff, 1992)
  • More similarity matrices
    • HELP to proper use of similarity matrices
    Software for representation of a pairwise sequence alignment:

  • LalnView at PBIL
  • LalnView at SIB/ExPASy
    Software to generate sequence logos:

  • plogo: Protein sequence logos at CBS/Denmark
  • slogo: RNA structure logos at CBS/Denmark
  • GENIO/logo: Sequence logos
  • WebLogo: Sequence logos at Berkeley
    Short online course about sequence comparisons:

  • Online course from "Biochemstry" (Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; ISBN: 0-7167-3051-0)
    Example of a pairwise sequence alignment:

  • beta globin: 
    mvhltpeeks avtalwgkvn vdevggealg rllvvypwtq rffesfgdls tpdavmgnpk
vkahgkkvlg afsdglahld nlkgtfatls elhcdklhvd penfrllgnv lvcvlahhfg
keftppvqaa yqkvvagvan alahkyh

  • Myoglobin: 
    mglsdgewql vlnvwgkvea dipghgqevl irlfkghpet lekfdkfkhl ksedemkase
dlkkhgatvl talggilkkk ghheaeikpl aqshatkhki pvkylefise ciiqvlqskh
pgdfgadaqg amnkalelfr kdmasnykel gfqg

  • SIM homology search: 

    Gap open penalty: 24
Gap extension penalty:  4
Comparison Matrix: BLOSUM62 
------------------------------------------------------------------------
23.8% identity in 122 residues overlap; Score: 91.0; Gap frequency: 0.0%

beta-Globin   25 GGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKG
Myoglobin     26 GQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKKKGHHEA
                 * * * **    * *   *  *  *   *        * **  ** *    *        

beta-Globin   85 TFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAH
Myoglobin     86 EIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMAS
                     *   *  *                 **       *    * *  *         * 

beta-Globin  145 KY
Myoglobin    146 NY
                  *
------------------------------------------------------------------------
40.9% identity in 22 residues overlap; Score: 38.0; Gap frequency: 0.0%

beta-Globin    4 LTPEEKSAVTALWGKVNVDEVG
Myoglobin      3 LSDGEWQLVLNVWGKVEADIPG
                 *   *   *   ****  *  *
------------------------------------------------------------------------


    Gap open penalty: 12
Gap extension penalty:  4
Comparison Matrix: BLOSUM62 
------------------------------------------------------------------------
25.5% identity in 145 residues overlap; Score: 103.0; Gap frequency: 1.4%

beta-Globin    4 LTPEEKSAVTALWGKVNVDEVGG--EALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
Myoglobin      3 LSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDL
                 *   *   *   ****  *  *   * * **    * *   *  *  *   *        

beta-Globin   62 KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
Myoglobin     63 KKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPG
                 * **  ** *    *            *   *  *                 **      

beta-Globin  122 EFTPPVQAAYQKVVAGVANALAHKY
Myoglobin    123 DFGADAQGAMNKALELFRKDMASNY
                  *    * *  *         *  *
------------------------------------------------------------------------
    Sequence examples:

  • Database of amino acid sequences via Entrez
  • Database of nucleotide sequences via Entrez

  • Bacteriorhodopsin from Halobacterium salinarium: Seven-helix bundle protein
  • TonB from Escherichia coli: Protein with N-terminal transmembrane helix
  • Maltose-binding protein from Escherichia coli: Protein with N-terminal signal sequence for secretion into the periplasmic space
  • OmpA from Escherichia coli: Two-domain protein: the N-terminal protein domain is embedded into the outer membrane in form of an 8-stranded β barrel while the C-terminal protein domain is found in the periplasmic space
    Abbreviations:

  • AMAS: Analyse Multiply Aligned Sequences
  • BCM: Baylor College of Medicine
  • BEAUTY: BLAST Enhanced Alignment Utility
  • BLAST: Basic Local Alignment Search Tool
  • BLOSUM: Blocks Substitution-Matrix
  • CINEMA: Color INteractive Editor for Multiple Alignments
  • COACH: COmparison of Alignments by Constructing HMMs
  • COFFEE: Consistency based Objective Function For alignmEnt Evaluation
  • COMPASS: COmparison of Multiple Protein Alignments with Assessment of Statistical Significance
  • ExPASy: Expert Protein Analysis System
  • FFAS03: Fold and Function Assignment System
  • MAFFT: Multiple Alignment using Fast Fourier Transform
  • MSA: Multiple Sequence Alignment
  • NIH: National Institute of Health
  • PAM: Percent Accepted Mutation
  • PIMA: Pattern-Induced Multiple-sequence Alignment program
  • PRALINE: PRofile ALIgNEment
  • SAGA: Sequence Alignment by Genetic Algorithm
  • SSMAL: Shuffled Similarities with Multiple ALignments

 

Latest update: October 14, 2009

Ralf Koebnik
Institut de recherche pour le dèveloppement
UMR 5096, CNRS-UP-IRD
911, Avenue Agropolis, BP 64501
34394 Montpellier, Cedex 5
FRANCE
Phone: +33 (0)4 67 41 62 28
Fax: +33 (0)4 67 41 61 81
Email: koebnik(at)gmx.de
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