Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

doi:10.1186/1471-2164-9-335

BMC Genomics

Volume 9

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Research article

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

Albert Pallejà¹^,2 , Eoghan D Harrington² and Peer Bork²^,3

¹Biochemistry and Biotechnology Department, Rovira i Virgili University, C/Marcel·lí Domingo s/n, 43007 Tarragona, Catalunya, Spain

²European Molecular Biological Laboratory, Meyerhofstrasse, 1, 69012 Heidelberg, Germany

³Max Delbrück Centre for Molecular Medicine, Berlin-Buch, Robert-Rössle-Strasse 10, D-13092 Berlin, Germany

author email corresponding author email

BMC Genomics 2008, 9:335doi:10.1186/1471-2164-9-335


Published:	15 July 2008

Additional files

Additional file 1:

The 968 overlaps manually analysed. The co-directional, convergent and divergent overlaps analysed. They are separated depending on the orientation of the pair. The genes identification is made joining the Taxonomy ID of the species which contains the gene and the gene name separated by a dot. The columns are the upstream and the downstream gene ids, the functions of the protein encoded in the genes, the orientation, the overlapping length and the type of misannotation. Notice that the types of misannotations are described at the end of each of the lists.

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Additional file 2:

Number of misannotations per genome in each category. Summary of the mispredicted overlaps found within the genome of each species sorted by categories.

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Additional file 3:

Misannotations related to some genome features. Table summarizing the genomes with more misannotations and some features of the genome such as genome length, gene content, GC content, sequencing method, annotating method and sequence date.

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Additional file 4:

Start codons analysis. Study of the start codons usage found among the three normal gene sets (random set I, II and II), which contains well-characterized non-overlapping genes randomly selected, and within the mispredicted start codon gene set. The usage and percentage of usage of each alternative start codon considered (AUG, GUG, UUG, other) is shown in the rows.

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