slides-alignment-1 - String Alignment I Computational...

Info icon This preview shows pages 1–6. Sign up to view the full content.

View Full Document Right Arrow Icon
Computational Biology - p.1/26 String Alignment I Computational Biology, Department Informatik ETH Zentrum
Image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Computational Biology - p.2/26 Organization What is an alignment? How do we score an alignment? Model (Markovian) Scoring function (Mutation Matrices) What algorithm do we use to align? Dynamic Programming Review of Last Week Proteins- strings with alphabet of 20 amino acids ACDEFGHIKLMNPQRSTVWY DNA- strings with alphabet over 4 nucleotide bases ACGTU DNA codes for protein 3 DNA nucleotides together make a "codon" which codes for 1 amino acid Genetic code is 64 codons translated into amino acids coding DNA has a "reading frame" - the correct place to start reading 3 bases G C G T G T A A A T G A \ \ < A > < Y > < K > < s t op > \\ < R > < V > < N > \\ < V > <s > < M > \ \
Image of page 2
Computational Biology - p.3/26 Genetic Code GGG G Gly AGG R Arg CGG R Arg UGG W Trp GGA G Gly AGA R Arg CGA R Arg UGA Stop GGC G Gly AGC S Ser CGC R Arg UGC C Cys GGU G Gly AGU S Ser CGU R Arg UGU C Cys GAG E Glu AAG K Lys CAG Q Gln UAG Stop GAA E Glu AAA K Lys CAA Q Gln UAA Sto p GAC D Asp AAC N Asn CAC H His UAC Y Tyr GAU D Asp AAU N Asn CAU H His UAU Y Tyr GCG A Ala ACG T Thr CCG P Pro UCG S Ser GCA A Ala ACA T Thr CCA P Pro UCA S Ser GCC A Ala ACC T Thr CCC P Pro UCC S Ser GCU A Ala ACU T Thr CCU P Pro UCU S Ser GUG V Val AUG M Met CUG L Leu UUG L Leu GUA V Val AUA I Ile CUA L Leu UUA L Leu GUC V Val AUC I Ile CUC L Leu UUC F Phe GUU V Val AUU I Ile CUU L Leu UUU F Phe
Image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Computational Biology - p.4/26 What is an alignment? [Rice, Mosquito] triosephosphate isomerase lengths=55,53 simil=117.7, PAM dist=117.766, offsets=-936190011,-9361895 _ identity=36.4%, similarity=18.2% NGTTDQVDKIVKILNEGQIASTDVVEVVVSPPYVFLPVVKSQLRPEIQVAAQNCW || .... !..!.|!|..|.!.:. .||||. | .!|.:.!|||...! ||||||! NGDKASIADLCKVLTTGPLNAD TEVVVGCPAPYLTLARSQLPDSVCVAAQNCY __ represents an evolutionary relationship aligns amino acids that diverged from the same residue in ancestor shows accepted substitutions since divergence proteins evolve under functional constraints - destroy function =? death "correct" alignment represents actual events- substitutions, indels impossible to verify -> take alignment with the highest probability that the alignment is correct under our model
Image of page 4
Computational Biology - p.5/26 Types of Alignments Protein-Protein (above) DNA/protein - align all 6 (3 forward, 3 backward) reading frames against protein must look for gaps and frameshifts within codons - complicated - done by Lukas Knecht DNA/DNA alignments • 
Image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Image of page 6
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern