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Local Sequence Alignment Variants: Finding Optimal Segment Pairs

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Discover the significance and applications of local sequence alignment, particularly in database searches using BLAST. Learn about high scoring segment pairs (HSPs) and the concept of PSI-BLAST for iterative improvements.

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Local Sequence Alignment Variants: Finding Optimal Segment Pairs

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  1. Paarweises Sequenz-Alignment Variante: Lokales Alignment. Sinnvoll, wenn Sequenzen nur lokale Homologie haben. Seq1CTAATTAATGCACAGTTAGGAATTAGAAATGA Seq2 GGGACATGGCAGTGACTGACCATGA

  2. Paarweises Sequenz-Alignment Variante: Lokales Alignment. Sinnvoll, wenn Sequenzen nur lokale Homologie haben. Seq1 CTAATTAATG-CACAGTTAGGAATTAGAAATGA Seq2GGGAC ATGGCA--GTGACTGACCATGA Aligne Paar von Segmenten der Sequenzen; ignoriere den Rest.

  3. Paarweises Sequenz-Alignment Ziel beim lokalen Alignment: Finde Paar von Segmenten, so dass Alignment der Segmente maximalen Score hat. Wichtigste Anwendung: Datenbank suche: Finde Sequenzen in der Datenbank, die zu gegebener Sequenz (Anfrage-Sequenz, query sequence) ähnlich sind.

  4. Paarweises Sequenz-Alignment Exaktes lokales Alignment zu zeitaufwendig. Schnelles Datenbank-Suchprogramm: BLAST - Basic Local Alignment Search Tool Stephen Altschul et al, JMB, 1990 21.778 Zitate in der Literatur ! Wichtigstes Werkzeug in der Bioinformatik!

  5. Paarweises Sequenz-Alignment

  6. Paarweises Sequenz-Alignment NCBI – National Center of Biotechnological Information

  7. Paarweises Sequenz-Alignment BLAST - Basic Local Alignment Search Tool Idee: Finde lokale Alignments ohne Gaps (HSPs – high scoring segment pairs). • Suche kurze Wort-Paare (feste Länge) • Dehne Wort-Paare aus, bis Score abfällt • Berechne Wahrscheinlichkeit, HSP per Zufall zu finden: e-value, p-value

  8. Paarweises Sequenz-Alignment Suche nach Wort-Paaren: Seq1 CTAATTAATGCACAGTTAGGAATTAGAAATGA Seq2 GGGACATGGCAGTGACTGAATACACACCATGA

  9. Paarweises Sequenz-Alignment Suche nach Wort-Paaren: Seq1 CTAATTAATGCACAGTTAGGAATTAGAAATGA Seq2 GGGACATGGCAGTGACTGAATACACACCATGA

  10. Paarweises Sequenz-Alignment Ausdehnung gefundener Wort-Paare: Seq1 CTAATTAATGCACAGTTAGGAATTAGAAATGA Seq2 GGGACATGGCAGTGACTGAATACACACCATGA

  11. Paarweises Sequenz-Alignment Ausdehnung gefundener Wort-Paare: Seq1 CTAATTAATGCACAGTTAGGAATTAGAAATGA Seq2 GGGACATGGCAGTGACTGAATACACACCATGA

  12. Paarweises Sequenz-Alignment Ausdehnung gefundener Wort-Paare: Seq1 CTAATTAATGCACAGTTAGGAATTAGAAATGA Seq2 GGGACATGGCAGTGACTGAATACACACCATGA

  13. Paarweises Sequenz-Alignment Ausdehnung gefundener Wort-Paare: Seq1 CTAATTAATGCACAGTTAGGAATTAGAAATGA Seq2 GGGACATGGCAGTGACTGAATACACACCATGA TTAATGCACA TGAATACACA High-scoring segment pair (HSP)

  14. Paarweises Sequenz-Alignment

  15. Paarweises Sequenz-Alignment

  16. Paarweises Sequenz-Alignment

  17. Paarweises Sequenz-Alignment Verbesserung: PSI-BLAST – Position Specific Iterative BLAST: (18.708 Zitate in der Literatur!)

  18. Paarweises Sequenz-Alignment PSI-BLAST – Position Specific Iterative BLAST: • “normale” DB-Suche mit BLAST • Bilde Positions-Gewichts-Matrix (PWM) aus “Treffern” • Suche mit PWM nach neuen “Treffern” • Bilde verbesserte PWM … u.s.w.

  19. Paarweises Sequenz-Alignment

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