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Evolutionary Bioinformatics

Synopsis: An open access, peer reviewed electronic journal that covers computational evolutionary biology and evolutionary bioinformatics.


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Aims and scope:

Evolutionary Bioinformatics is an international, peer-reviewed journal focusing on evolutionary bioinformatics. There is growing awareness that to understand organismal form and function, through the use of molecular, genetic, genomic, and proteomic data, due consideration must be given to an organism's evolutionary context - history constrains the path an organism is obliged to take, and leaves an indelible mark on its component parts. Evolutionary Bioinformatics publishes papers on all aspects of computational evolutionary biology and evolutionary bioinformatics.

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All submissions to this journal, with the exception of editorials and dedications (obituaries), are subject to rigorous peer review by a minimum of two peer reviewers who demonstrate current research experience in the paper's subject area.  Reviewers are required to provide in-depth, fair and objective reviews.  They may not act as reviewers if they are in a conflict of interest.  All final publishing decisions are made by the Editor in Chief or Associate Editor.

Official journal of the Bioinformatics Institute:

Evolutionary Bioinformatics was established as the official journal of The Bioinformatics Institute.  The Institute is a joint-venture between the University of Auckland, situated in New Zealand’s largest city, and AgResearch, New Zealand’s largest Crown Research Institute. Allen Rodrigo, Professor of Computational Biology and Bioinformatics, is the Institute’s Director, and it was at his initiative that the journal was established.

Working in collaboration with The Institute is Libertas Academica, a publishing firm committed to high editorial standards, open access publishing methodologies and superior user-service standards. There is much work involved ‘behind-the-scenes’ that goes towards the finished result seen by readers of Evolutionary Bioinformatics. Key amongst this work, which also includes attracting the best submissions, supervising effective peer review and typesetting, is gaining acceptance for indexing by outside organizations.

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As of April 7 2008, the US NIH Public Access Policy requires that all peer reviewed articles resulting from research carried out with NIH funding be deposited in the Pubmed Central archive.

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ISSN: 1176-9343


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Positional Homology in Bacterial Genomes

Authors: Ingrid J. Burgetz, Salimah Shariff, Andy Pang and Elisabeth R. M. Tillier
Publication Date: 14 Jan 2007
Evolutionary Bioinformatics 2006:2 77-90

Ingrid J. Burgetz1, Salimah Shariff2, Andy Pang2 and Elisabeth R. M. Tillier3*

3Dept. of Medical Biophysics, University of Toronto and 1,2,3 Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada

Abstract: In comparative genomic studies, syntenic groups of homologous sequence in the same order have been used as supplementary information that can be used in helping to determine the orthology of the compared sequences. The assumption is that orthologous gene copies are more likely to share the same genome positions and share the same gene neighbors. In this study we have defined positional homologs as those that also have homologous neighboring genes and we investigated the usefulness of this distinction for bacterial comparative genomics. We considered the identification of positionaly homologous gene pairs in bacterial genomes using protein and DNA sequence level alignments and found that the positional homologs had on average relatively lower rates of substitution at the DNA level (synonymous substitutions) than duplicate homologs in different genomic locations, regardless of the level of protein sequence divergence (measured with non-synonymous substitution rate). Since gene order conservation can indicate accuracy of orthology assignments, we also considered the effect of imposing certain alignment quality requirements on the sensitivity and specificity of identification of protein pairs by BLAST and FASTA when neighboring information is not available and in comparisons where gene order is not conserved. We found that the addition of a stringency filter based on the second best hits was an efficient way to remove dubious ortholog identifications in BLAST and FASTA analyses. Gene order conservation and DNA sequence homology are useful to consider in comparative genomic studies as they may indicate different orthology assignments than protein sequence homology alone.



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