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Home / Proceedings / Proceedings of the Twentieth International Conference on Machine Learning, 1995 / Book One

A Distance-Based Block Searching Algorithm

March 15, 2023

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Authors

Marie-France Sagot

Alain Viari

and Henri Soldano

DOI:


Abstract:

We present in this paper an algorithm for the multiple comparison of a set of protein sequences. Our approach is that of peptide matching and consists in looking for all the words that occur approximatively in at least q of the sequences in the set, where q is a parameter. Words are compared by using a reference object called a model, that is itself a word over the alphabet of the amino acids, and the comparison between a model and a word is based on w-length words instead of single symbols. This idea is similar to the one used in the Blast program in the case of pairwise comparisons. Two w-length words are considered to be related if an alignment without gaps of the two using a similarity matrix has a score greater than a certain threshold value t. In our case, we say that a k-length word u is an occurrence of a model m of the same length if every w-length subword of u is related to the corresponding subword of m in the sense given above. If a model m has occurrences in at least q of the sequences of the set, m is said to occur in the set. In percentage terms, the value of q may correspond to something as small as 5% of the sequences (search for recurrent words in a set of non homologuous proteins) or as high as 70-100% (establishment of a list of all similar words as a first step in a multiple alignment program). The algorithm presented here is an efficient and exact way of looking for all the models, of a fixed length k or of the greatest possible length kmax, that occur in a set of sequences. It can work with any kind of scoring matrix and an extension of the algorithm allows for the introduction of gaps between a model and its occurrences.

Topics: ISMB

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HOW TO CITE:

Marie-France Sagot||Alain Viari||and Henri Soldano A Distance-Based Block Searching Algorithm Proceedings of the Twentieth International Conference on Machine Learning, 1995 (1995) .

Marie-France Sagot||Alain Viari||and Henri Soldano A Distance-Based Block Searching Algorithm ISMB 1995, .

Marie-France Sagot||Alain Viari||and Henri Soldano (1995). A Distance-Based Block Searching Algorithm. Proceedings of the Twentieth International Conference on Machine Learning, 1995, .

Marie-France Sagot||Alain Viari||and Henri Soldano. A Distance-Based Block Searching Algorithm. Proceedings of the Twentieth International Conference on Machine Learning, 1995 1995 p..

Marie-France Sagot||Alain Viari||and Henri Soldano. 1995. A Distance-Based Block Searching Algorithm. "Proceedings of the Twentieth International Conference on Machine Learning, 1995". .

Marie-France Sagot||Alain Viari||and Henri Soldano. (1995) "A Distance-Based Block Searching Algorithm", Proceedings of the Twentieth International Conference on Machine Learning, 1995, p.

Marie-France Sagot||Alain Viari||and Henri Soldano, "A Distance-Based Block Searching Algorithm", ISMB, p., 1995.

Marie-France Sagot||Alain Viari||and Henri Soldano. "A Distance-Based Block Searching Algorithm". Proceedings of the Twentieth International Conference on Machine Learning, 1995, 1995, p..

Marie-France Sagot||Alain Viari||and Henri Soldano. "A Distance-Based Block Searching Algorithm". Proceedings of the Twentieth International Conference on Machine Learning, 1995, (1995): .

Marie-France Sagot||Alain Viari||and Henri Soldano. A Distance-Based Block Searching Algorithm. ISMB[Internet]. 1995[cited 2023]; .


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