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huda

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  • Favorite Area of Science
    DNA sequence

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  1. thanks all what u said , I know it. I want to know if I have this matrix : 10 2 4 2 5 3 4 3 6 if the diagonal in similarity matrix must be 1 so the matrix will be: 1 2/10 4/10 2/5 1 3/5 4/6 3/6 1 is that what u mean? thanks
  2. No, I do not mean the max scor is zero, but mean if I have to fill diagonal with elements it must be the max score that result from comparison the elment with itself. Now, u mean similarity is 1-distance , this is why be 1. Please, if u have any reference about what you said indicate for it. thanks
  3. why the diagonal must be 1? if do alignment sequence and compare the object with itself , it get max score because there is fully matching. please, clarify that. thanks
  4. hi, what are the numbers have to bee in similarity matrix? is it be the the large real vaule of comparison the element with itself? thanks
  5. hi, can I find code in matlab of agglomerative clustering method? thanks
  6. hi, what this distance metric is called that equal ∑ ABS(ai-bi) thanks
  7. huda

    distance metric

    what I have to do now?
  8. hi, If I have similarity matrix that I got it from sequence alignment, where each element of this matrix repersent the rate of similarity .i.e the max score represent mas similarity. say n*n symmetric that show the rate of similarity among n objects . ex. x=[10 3 2 3 6 4 2 4 5]; here obj. 1 is most similar to obj. 2 because the max score except diagonal(10) is 3 and so on. the diagonal here is represent the comparison the object with itsel so has the max value if I used distance metric such euclidean distance to cluster these objects, is it best to set the diagonal to zero, or leave it ? by the way , which the best way to cluster the similarity matrix that result from sequence alignment?
  9. Regarding smith_waterman algorithm(local alignment),the main difference to the Needleman–Wunsch algorithm is that negative scoring matrix cells are set to zero, which renders the (thus positively scoring) local alignments visible
  10. thanks, how can asssign value for match, mismatch, gap sometime gap is given -1, and other time 0, or -2 the same thing for match , sometime is given 2 and i other time 1. how can know the best? when I did sequence alignment, I skipped the comparison the element with itself, so get zeros in diagonal. Is the processing is right? which the best method to do clustering given similarity matrix of sequence alignment? and if similarity matrix has zeros in diagonal , is that has affecting the clustering results?
  11. hi, I applied sequence alignment with dataset of social networks, and I got similarity matrix. for ex. z is similarity matrix with size 3*3 z=[0 2 3; 2 0 4; 3 4 0]; when I did sequence alignment, I skipped the comparison the element with itself, so get zeros in diagonal. Is the processing is right? which the best method to do clustering given similarity matrix of sequence alignment? and if similarity matrix h as zeros in diagonal , is that has affecting the clustering results? thanks in advance
  12. hi, is the score of sequence alignmnet can be negative when alignmnet non biological sequence? Note: whether global or local alignmnet thanks in advance
  13. hi, I have to use newman algorithm in my work in PhD thesis. I have no idea about it. so, I would like to know : is newman algorithm clustering method or it is used after clustering method to remove the edges? thanks
  14. Are there anybody know any paper work particle swarm opt. with local sequence alignment but not global seq. alignmnet . I did not find any paper use pso with local alignment. please, I badly need any information about it. thanks, huda
  15. hi, I'm working in sequence alignment with non biological sequences. I read much about gap penlty, each author deal with gaps differently. how i can decide which policy is best? thanks, huda
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