Abstract
We consider the problem of finding candidates for regulatory elements of alternative splicing events from orthologous genes, using phylogenetic footprinting. The problem is formulated as follows: We are given orthologous sequences P1, . . . , Pa and N1, . . . , N b from a + b different species, and a phylogenetic tree relating these species. Assume that for i = 1, . . . , a, Pi is known to have some alternative splicing events, although Nj does not have any alternative splicing events. Our objective is to find all sets of substrings s1, . . . , sa of P1, . . . , Pa such that s1, . . . ,sa are similar to each other to some extent, and such that any substrings of N1, . . . , Nb are not similar to s1, . . . , sa. To this aim, we have modified the phylogenetic footprinting algorithm given by Blanchette et al. to solve our problem. We report the results of our preliminary computational experiments on several sets of orthologous genes of the five species, H.sapiens, M.musculus, D.melanogaster, C.elegans, and A.thaliana. It is interesting that many of the substrings selected by our algorithm from the coding sequences of H.sapiens are substrings in the intronic sequences flanking the alternatively spliced exons of the coding sequence. This result implies that regulatory elements of alternative splicing events would be located in intronic sequences flanking the alternatively spliced exons.
| Original language | English |
|---|---|
| Pages (from-to) | 147-158 |
| Number of pages | 12 |
| Journal | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
| Volume | 3240 |
| Publication status | Published - Dec 1 2004 |
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All Science Journal Classification (ASJC) codes
- Theoretical Computer Science
- Computer Science(all)
Cite this
Searching for regulatory elements of alternative splicing events using phylogenetic footprinting. / Shigemizu, Daichi; Maruyama, Osamu.
In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 3240, 01.12.2004, p. 147-158.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Searching for regulatory elements of alternative splicing events using phylogenetic footprinting
AU - Shigemizu, Daichi
AU - Maruyama, Osamu
PY - 2004/12/1
Y1 - 2004/12/1
N2 - We consider the problem of finding candidates for regulatory elements of alternative splicing events from orthologous genes, using phylogenetic footprinting. The problem is formulated as follows: We are given orthologous sequences P1, . . . , Pa and N1, . . . , N b from a + b different species, and a phylogenetic tree relating these species. Assume that for i = 1, . . . , a, Pi is known to have some alternative splicing events, although Nj does not have any alternative splicing events. Our objective is to find all sets of substrings s1, . . . , sa of P1, . . . , Pa such that s1, . . . ,sa are similar to each other to some extent, and such that any substrings of N1, . . . , Nb are not similar to s1, . . . , sa. To this aim, we have modified the phylogenetic footprinting algorithm given by Blanchette et al. to solve our problem. We report the results of our preliminary computational experiments on several sets of orthologous genes of the five species, H.sapiens, M.musculus, D.melanogaster, C.elegans, and A.thaliana. It is interesting that many of the substrings selected by our algorithm from the coding sequences of H.sapiens are substrings in the intronic sequences flanking the alternatively spliced exons of the coding sequence. This result implies that regulatory elements of alternative splicing events would be located in intronic sequences flanking the alternatively spliced exons.
AB - We consider the problem of finding candidates for regulatory elements of alternative splicing events from orthologous genes, using phylogenetic footprinting. The problem is formulated as follows: We are given orthologous sequences P1, . . . , Pa and N1, . . . , N b from a + b different species, and a phylogenetic tree relating these species. Assume that for i = 1, . . . , a, Pi is known to have some alternative splicing events, although Nj does not have any alternative splicing events. Our objective is to find all sets of substrings s1, . . . , sa of P1, . . . , Pa such that s1, . . . ,sa are similar to each other to some extent, and such that any substrings of N1, . . . , Nb are not similar to s1, . . . , sa. To this aim, we have modified the phylogenetic footprinting algorithm given by Blanchette et al. to solve our problem. We report the results of our preliminary computational experiments on several sets of orthologous genes of the five species, H.sapiens, M.musculus, D.melanogaster, C.elegans, and A.thaliana. It is interesting that many of the substrings selected by our algorithm from the coding sequences of H.sapiens are substrings in the intronic sequences flanking the alternatively spliced exons of the coding sequence. This result implies that regulatory elements of alternative splicing events would be located in intronic sequences flanking the alternatively spliced exons.
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M3 - Article
VL - 3240
SP - 147
EP - 158
JO - Lecture Notes in Computer Science
JF - Lecture Notes in Computer Science
SN - 0302-9743
ER -