dorsal/arxiv
View SchemaCo-expression of statistically over-represented peptides in proteomes: a key to phylogeny ?
| Authors | Luca Ferraro, Andrea Giansanti, Giovanni Giuliano, Vittorio Rosato |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0410011 |
| URL | https://arxiv.org/abs/q-bio/0410011 |
Abstract
It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a phylogenetic distance is introduced and the corresponding distance matrix between proteomes is constructed. From the distance matrix a phylogenetic tree is inferred, following a standard procedure. It compares well with a reference tree deduced from a distance matrix obtained from the alignment of ribosomal RNA sequences. Our results are consistent with the hypothesis that biological evolution manifests itself with a modulation of basic correlations between shared peptides of short length, present in protein sequences. Moreover, the simple procedure we propose reconfirms that it is possible, sampling entire proteomes, to average the effects of lateral gene transfer and infer reasonable phylogenies.
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"abstract": "It is proposed that the co-expression of statistically significant motifs\namong the sequences of a proteome is a phylogenetic trait. From the\nco-expression matrix of such motifs in a group of prokaryotic proteomes a\nsuitable definition of a phylogenetic distance is introduced and the\ncorresponding distance matrix between proteomes is constructed. From the\ndistance matrix a phylogenetic tree is inferred, following a standard\nprocedure. It compares well with a reference tree deduced from a distance\nmatrix obtained from the alignment of ribosomal RNA sequences. Our results are\nconsistent with the hypothesis that biological evolution manifests itself with\na modulation of basic correlations between shared peptides of short length,\npresent in protein sequences. Moreover, the simple procedure we propose\nreconfirms that it is possible, sampling entire proteomes, to average the\neffects of lateral gene transfer and infer reasonable phylogenies.",
"arxiv_id": "q-bio/0410011",
"authors": [
"Luca Ferraro",
"Andrea Giansanti",
"Giovanni Giuliano",
"Vittorio Rosato"
],
"categories": [
"q-bio.MN",
"q-bio.GN",
"q-bio.PE"
],
"title": "Co-expression of statistically over-represented peptides in proteomes: a key to phylogeny ?",
"url": "https://arxiv.org/abs/q-bio/0410011"
},
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