II Curso Nacional de Gen

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comparative gene prediction
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sequence conservation andcoding function
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sequence conservation and coding function
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Conservation betwen human and mousecoding and
non-coding regions
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comparative gene prediciton

• rosseta (Batzoglou et al., 2000)
• cem (Bafna and Huson, 2000)
• sgp1 (Wiehe et al., 2000)
• twinscan (Korf et al., 2001)
• slam (Patcher et al., 2001)
• doublescan (Meyer and Durbin, 2002)
• sgp2 (Parra et al., 2003)

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comparative gene prediction

• THE GENE PREDICTION IS THE RESULT OF THE
  SEQUENCE ALIGNMENT
• given two homologous genomic sequences, infer the
  exonic structure in each sequence maximizing the
  score of the alignment of the resulting amino
  acid sequences.
• This problem is usually solved through a complex
  extension of the classical
• dynamic programming algorithm for sequence
  alignment.
• blayo et al., 2002
• pedersen and scharl, 2002

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comparative gene prediction

• 2. GENE PREDICTION AND SEQUENCE ALIGNMENT ARE
  PRODUCED SIMULTANIOUSLY
• given two homologous genomic sequences, Pair
  hidden Markov Models for sequence alignment, and
  Generalized HMMs (GHMMs) for gene prediction are
  combined into the so-called Generalized Pair HMMs
• progen novichkov et al., 2001
• slam pachter et al, 2001
• doublescan meyer and durbin, 2002

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comparative gene prediction

• 3. GENE PREDICTION IS SEPARATED FROM SEQUENCE
  ALIGNMENT
• first, the alignment is obtained between two
  homologous genomic sequences using some generic
  sequence alignment program, such as tblastx, sim4
  or glass
• then, gene structures are predicted that are
  compatible with this alignment, meaning that
  predicted exons fall in the aligned regions.
• rosseta batzoglou et al., 2000
• cem bafna and huson, 2000
• sgp-1 wiehe et al., 2001

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comparative gene prediction

• 4. GENE PREDICTION IS (EVEN MORE) SEPARATED FROM
  SEQUENCE ALIGNMENT
• This approach does not require the comparison of
  two homologous genomic sequencs. Rather, a query
  sequence from a target genome is compared
  against a collection of sequence from a second
  (informant, reference) genome and the results of
  the comparison are used to modify the scores of
  the exons produced
• by underlying ab initio'' gene prediction
  algorithms.
• twinscan korf et al., 2001
• sgp-2 parra et al., 2003

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comparative gene prediction
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comparative gene prediction
Accuracy on human chromosome 22