By Behshad Behzadi, Martin Vingron (auth.), Guillaume Bourque, Nadia El-Mabrouk (eds.)

ISBN-10: 3540445293

ISBN-13: 9783540445296

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"Comparative genomics is a thrilling new box of bioinformatics facing difficulties of important value for lots of parts in biology. … This quantity includes the 17 absolutely refereed papers offered on the fourth assembly, held in Montreal in September 2006. … I think of this booklet crucial for libraries aiming to help examine in any box of bioinformatics." (N. Sapidis, ACM Computing stories, Vol. forty nine (4), April, 2008)

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Additional info for Comparative Genomics: RECOMB 2006 International Workshop, RCG 2006 Montreal, Canada, September 24-26, 2006 Proceedings

Example text

W´ ojtowicz and J. Tiuryn size distribution of gene families in a genome seems to be invariant over time [17,18,6,7,23,8,16,20,22]. e. in the total absence of selective pressure or at least we have to assume that at the genome level selective pressure does not substantially change the shape of gene family size distribution. We are fully aware that such a purely neutralistic model cannot be truly realistic. However, it explains the biological observations and it can be very useful in further discussions in this topic.

Algorithmical point of view, the set of all common intervals of two sequences can be computed in quadratic time [22]. Note however that gene deletions or insertions, that are natural evolutionary events, can destroy common intervals, and we discuss this issue in Section 4. In Section 2, we describe precisely our method to compute a gene matching. In Section 3, we present two experimental studies of our method. We first consider 8 genomes of γ-proteobacteria, and we compare the results of our method with the LCS method of [5]; this experiment raises interesting facts about the properties of these two notions of conserved structures in the comparison of more than two genomes.

The results are given in Tables 1 and 2. Table 1. 2 First, it is interesting to notice that the number of true positives gene pairs in consistent components decreases when one reduces the minimal length of matched LCS, which is expected, while it increases when one reduces the Inferring Positional Homologs with Common Intervals of Sequences 31 Table 2. Distribution of perfect and imperfect components by size Perfect components of size 8 Imperfect components of size 8 Perfect components of size 7 Imperfect components of size 7 Perfect components of size 6 Imperfect components of size 6 Perfect components of size 5 Imperfect components of size 5 Perfect components of size 4 Imperfect components of size 4 Perfect components of size 3 Imperfect components of size 3 LCS1 258 19 209 34 157 32 206 32 236 65 465 70 LCS2 138 15 155 13 145 24 269 39 290 59 726 90 LCS3 71 9 100 9 107 19 199 24 246 49 815 80 CI1 254 29 218 37 172 46 222 44 253 77 509 87 CI2 259 30 227 45 185 57 251 76 344 178 551 129 CI3 263 32 244 86 215 114 299 135 368 186 573 134 minimum side of discarded boxes when using common intervals.

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Comparative Genomics: RECOMB 2006 International Workshop, RCG 2006 Montreal, Canada, September 24-26, 2006 Proceedings by Behshad Behzadi, Martin Vingron (auth.), Guillaume Bourque, Nadia El-Mabrouk (eds.)


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