Paper Info
Title
Comparative genomics study of inverted repeats in bacteria.
Abstract
Motivation: Comparative genomics provides a powerful way to investigate regularities and differences observed at DNA level across species. Here we study the number and location of inverted repeats occurring in complete genomes of bacteria. Inverted repeats are compatible with the formation of hairpin structures in the messenger RNA. Some of these structures are known to be rho-independent intrinsic terminators. Results: We investigate the number of inverted repeats observed in 37 complete genomes of bacteria. The number of inverted repeats observed is much higher than expected using Markovian models of DNA sequences in most of the eubacteria. By using the information annotated in the genomes we discover that in most of the eubacteria the inverted repeats of stem length longer than 8 nucleotides preferentially locate near the 3' end of the nearest coding regions. We also show that IRs characterized by large values of the stem length locate preferentially in short non-coding regions bounded by two 3' ends of convergent genes. By using the program TransTerm recently introduced to predict transcription terminators in bacterial genomes, we conclude that only a part of the observed inverted repeats fullfils the model requirements characterizing rho-independent termination in several genomes.
Year
DOI
Venue
2002
10.1093/bioinformatics/18.7.971
BIOINFORMATICS
Keywords
Field
DocType
bacterial genome,nucleotides,comparative genomics,inverted repeat,statistical mechanics,ribosomal protein,binding protein,dna sequence,messenger rna
Tandem repeat,Genome,Biology,Direct repeat,Inverted repeat,Coding region,Comparative genomics,DNA sequencing,Bioinformatics,Bacterial genome size
Journal
Volume
Issue
ISSN
18
7
1367-4803
Citations 
PageRank 
References 
5
0.55
0
Authors
3
Name
Order
Citations
PageRank
Fabrizio Lillo14110.66
Salvatore Basile250.55
Rosario N. Mantegna3344.72