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http://creativecommons.org/licenses/by-sa/2.0/. From Genes to Proteins (and a little bit about allignments). Prof:Rui Alves ralves@cmb.udl.es 973702406 Dept Ciencies Mediques Basiques, 1st Floor, Room 1.08

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  1. http://creativecommons.org/licenses/by-sa/2.0/

  2. From Genes to Proteins(and a little bit about allignments) Prof:Rui Alves ralves@cmb.udl.es 973702406 Dept Ciencies Mediques Basiques, 1st Floor, Room 1.08 Website of the Course:http://web.udl.es/usuaris/pg193845/Courses/Bioinformatics_2007/ Course: http://10.100.14.36/Student_Server/

  3. (and a little about allignments) • How does blast work?

  4. How Does BLAST Really Work? • The BLAST programs improved the overall speed of searches while retaining good sensitivity (important as databases continue to grow) by breaking the query and database sequences into fragments ("words"), and initially seeking matches between fragments.

  5. BLAST Algorithm

  6. How Does BLAST Really Work? • Word hits are then extended in either direction in an attempt to generate an alignment with a score exceeding the threshold of "S".

  7. BLAST Algorithm

  8. Extending the High Scoring Segment Pair (HSP) Significance Decay Minimum Score Neighborhood Score Threshold

  9. BLAST Algorithm • Sequences are split into words (default n=3) • Speed, computational efficiency • Scoring of matches done using scoring matrices • HSP = high scoring segment pair • BLAST algorithm extends the initial “seed” hit into an HSP • Local optimal alignment • More than one HSP can be found

  10. Where does the score (S) come from? • The quality of each pair-wise alignment is represented as a score and the scores are ranked. • Scoring matrices are used to calculate the score of the alignment base by base (DNA) or amino acid by amino acid (protein). • The alignment score will be the sum of the scores for each position.

  11. Organization of the Talk • From cDNA sequence to protein sequence.

  12. Predicting protein sequence from DNA sequence • Protein sequence can be predicted by translating the cDNA and using the genetic code.

  13. Translating cDNA into protein sequence ATGTCTCTTATATGA… No Gene!!!!! Met Ser Leu Ile Ter

  14. Sometimes stop codons are not stop codons.

  15. Are there alternative genetic codes? • YES!!!!

  16. Flatworm mitochondria Echinoderm/Flatworm mitochondria Trematode mitochondria Ascidian mitochondria Vertebrate mitochondria Yeast mitochondria Invertebrate mitochondria

  17. Yeast mitochondria Candida

  18. Ciliate, Dasycladacean Hexamita

  19. Translating yeast mitochondrial cDNA into protein sequence ATGTCTCTTATATGA………SECIS sequence There is a Gene with a considerably different protein sequence from the one we would predict from the universal genetic code!!!!! Trp Ser Thr Met sCys Met Ser Leu Ile Ter

  20. What changed? • END→AA (16 events, all ter codons) • AA →END (3 events) • AA →AA’ (22 events, 3 AA)

  21. Conclusions • Translating DNA or mRNA sequence into proteins is easy but you need to be carefull as to which genetic code you need to use.

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