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Problems in Bioinformatics Motif Search & Protein Alignment Hariharane Ramasamy
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Motif Search Tool
5 to 20 ≈  3KB Gene Sequences of length 5-20 bases (exist on either side of the gene)  control the gene transcription. Such sequences often are over represented near the gene they regulate.  They co-ordinate in controlling the gene transcription. It is believed such short motifs are highly preserved due to their functionality and are transferred across organisms with minor changes.
Current Motif Tools ,[object Object],[object Object],[object Object],[object Object]
 
reg exp. e.g GGGWWW3CYS C | T Y  A | T W A | C | G V C | G S A | G R A | C | G | T N A | C M G | T K A | C | T H A | G | T D C | G | T B
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
 
 
 
 
 
 
 
Protein Sequence Alignment
[object Object],[object Object],[object Object],[object Object]
Smith Waterman Algorithm Where D ij  denotes the element in the matrix S ij  represents the similarity score between two amino acids. The similarity value is obtained by the number of properties common between two amino acids. (32 bit vector is use with 32 nd  bit denoting the gap bit.  w k   and  w l   represents penalty for introducing gap
 
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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Advanced Search Grammar Tool for locating non functional coding sequences in a genome

  • 1. Problems in Bioinformatics Motif Search & Protein Alignment Hariharane Ramasamy
  • 2.
  • 4. 5 to 20 ≈ 3KB Gene Sequences of length 5-20 bases (exist on either side of the gene) control the gene transcription. Such sequences often are over represented near the gene they regulate. They co-ordinate in controlling the gene transcription. It is believed such short motifs are highly preserved due to their functionality and are transferred across organisms with minor changes.
  • 5.
  • 6.  
  • 7. reg exp. e.g GGGWWW3CYS C | T Y A | T W A | C | G V C | G S A | G R A | C | G | T N A | C M G | T K A | C | T H A | G | T D C | G | T B
  • 8.
  • 9.  
  • 10.  
  • 11.  
  • 12.  
  • 13.  
  • 14.  
  • 15.  
  • 16.  
  • 17.  
  • 19.
  • 20. Smith Waterman Algorithm Where D ij denotes the element in the matrix S ij represents the similarity score between two amino acids. The similarity value is obtained by the number of properties common between two amino acids. (32 bit vector is use with 32 nd bit denoting the gap bit. w k and w l represents penalty for introducing gap
  • 21.  
  • 22.