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Sequenzvergleiche

Homologiesuche

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    Sequenzvergleiche im Internet:

    Dot-Matrizen

  • Examples of DotPlot Visualization Technique
  • DotPlot @ Uni Düsseldorf
  • DotPlot: Dotmatrix-Vergleich zweier Sequenzen (Not for Macintosh-Browser!)

    Klassiker

  • Needleman & Wunsch: Globales Alignment
  • Smith & Waterman: Lokales Alignment

    Paarweise Sequenzvergleiche

  • BCM: Paarweise Sequenzvergleiche: SIM, ALIGN/LALIGN, BLAST2, LAP2
  • ExPASy: Sequenzvergleiche: SIM, LALIGN (see below)
  • Sequence analysis Tools at EBI (see below)
    • EMBOSS Pairwise Alignment Algorithms (global and local)
    • Wise2 at EBI compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors
    • Advanced Wise2
    • 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 (IGH)
  • BLAST 2: Vergleich zweier Sequenzen am NIH
  • GLASS: GLobal Alignment SyStem
  • LALIGN: Finds multiple matching subsegments in two sequences (SIM-based code)
  • LFASTA: Local Alignment Tool for Nucleic Sequences
  • Palign: Protein alignment
  • SIM: Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW
  • SIM4: Program to align cDNA and genomic DNA
  • ToPlign (Toolbox for Protein ALignment): Paarweiser und multipler Sequenzvergleich

  • PRSS3: evaluates the significance of a protein sequence alignment

    Multiple Sequenzvergleiche

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

  • ClustalW at EBI
  • ClustalW at PBIL
  • ClustalW at EMBnet

  • 3DCoffee at CNRS Marseille
  • T-Coffee at EMBnet
  • DIALIGN: Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany
  • MAFFT at Genome Center of Japan
  • Match-Box at University of Namur, Belgium (nur Proteine!)
  • MSA: Multiple Sequence Alignment, at Washington University (OUTDATED)
  • Multalin at INRA
  • Multalin at PBIL (nur Proteine!)
  • MUSCA: Multiple sequence alignment using pattern discovery, at IBM (nur Proteine!)
  • MUSCLE: MUltiple Sequence Comparison by Log-Expectation
  • 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 zum Download)
  • SATCHMO: Simultaneous Alignment and Tree Construction using Hidden Markov mOdels (Software zum Download)
  • SSMAL: Shuffled Similarities with Multiple ALignments (Software zum Download) (OUTDATED)

    Profilvergleiche

  • COACH: COmparison of Alignments by Constructing HMMs (Software zum Download)
  • COMPASS: COmparison of Multiple Protein Alignments with Assessment of Statistical Significance
  • FFAS03: Fold and Function Assignment System
    Sequenzformate:

  • Beispiel eines SwissProt-Eintrags im FASTA-Format
  • Beispiel eines Multiplen Alignments im MSF-Format
    Ähnlichkeitsmatrizen:

  • PAM250: Percent Accepted Mutation-Matrix (Dayhoff et al., 1978)
  • BLOSUM62: Blocks Substitution-Matrix (Henikoff und Henikoff, 1992)
  • Weitere Ähnlichkeitsmatrizen
    • HELP zur Nutzung der Ähnlichkeitsmatrizen
    Software zur Repräsentation paarweiser Alignments:

  • LalnView at Lyon
  • LalnView at ExPASy
    Software zur Erzeugung von Sequenz-Logos:

  • plogo: Protein sequence logos at CBS/Denmark
  • slogo: RNA structure logos at CBS/Denmark
  • GENIO/logo: Sequence logos
  • WebLogo: Sequence logos at Berkeley
    Kurzer Online-Kurs über Sequenzvergleiche:

  • Online-Kurs, aus "Biochemstry" (Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; ISBN: 0-7167-3051-0)
    Beispiel eines paarweisen Sequenzvergleichs:

  • 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-Homologiesuche: 

    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
                  *    * *  *         *  *
------------------------------------------------------------------------
    Beispielsequenzen:

  • Aminosäuresequenz-Datenbank via Entrez
  • Nukleotidsequenz-Datenbank via Entrez

  • Bacteriorhodopsin von Halobacterium salinarium: 7 Helix-Bündel-Protein
  • TonB von Escherichia coli: Protein mit N-terminaler Transmembran-Helix
  • Maltose-binding protein von Escherichia coli: Protein mit N-terminaler Signalsequenz zur Sekretion ins Periplasma
  • OmpA von Escherichia coli: 2-Domänen-Protein: die N-terminale Proteindomäne ist in Form eines 8-strängigen beta-Fasses in die äussere Membran eingelagert; die C-terminale Proteindomäne befindet sich im Periplasma
    Abkürzungen:

  • 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
  • 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

 

Letzte Aktualisierung: 24. Oktober 2005

Ralf Koebnik
Institut für Genetik
Abt. Pflanzengenetik
Weinbergweg 10
06120 Halle/Saale
Telefon: 0345 / 55 26 293 (Büro) bzw. 296 (Labor)
Fax: 0345 / 55 27 151
Email: koebnik (at) gmx.de
Please replace (at) by @.

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