Biology Direct serves the life science research community as an open access, peer-reviewed online journal, providing authors and readers with an alternative to the traditional model of peer review. Biology Direct considers original research articles, hypotheses, comments, discovery notes and reviews in subject areas currently identified as those most conducive to the open review approach, primarily those with a significant non-experimental component.
- Eugene Koonin, NCBI, NLM, NIH
- Laura Landweber, Princeton University
- David Lipman, NCBI, NLM, NIH
The study analyzes nine motif finding Web tools for detecting binding site motifs in ChIP-Seq data. The detailed features of each tool, its approach, as well as its strengths and weaknesses are discussed.
The study points out several factors that can affect the results of motif finding. It discusses the role of peak calling, the influence of peak calling on motif finding and provides suggestions for optimizing peak calling results for motif detection.
Experiments have been performed on each motif finding Web tool using different ChIP-Seq datasets. The discovered motifs from each tool for the same dataset were validated and compared. The results reveal each tool reported a different number of discovered motifs for the same dataset with degrees of similarity vary.
The analysis shows the causes of various results reported by each tool in two aspects: (1) different tool implemented different approach and algorithms for motif finding, (2) each tool has its own parameters set up for finding motifs. It also reveals that each tool has its own advantages for detecting motifs that other tools may not discover. The analysis suggests that motifs reported by multiple tools for the same dataset are more reliable. Hence, multiple motif finding Web tools should be used for finding motifs.
Although many efforts have been dedicated for the development of motif finding Web tool, several improvements are still needed for improving research in motif detection. The study also points out these improvement aspects.
Based on a regression analysis which includes measurement errors and confidence intervals, genome size-time data for major phyla are found to be consistent with life having originated after Earth's formation.
The loss of information through the multiple processing steps of biological systems may explain the common scaling relations between inputs and outputs.
One of the major challenges in designing epitope or peptide-based vaccine is to induce desired interleukin, particularly induction of interferon-gamma is important for designing vaccine against intracellular pathogens.
The highly similar eukaryotic translation elongation factors 1A1 and
1A2 show a surprising enhancement of post-translational modification proximal to surface clusters of sequence variation on their modelled structures informing on their functional divergence.
Drug discovery is a costly and time consuming process that can be improve significantly with the help of software drugmint developed for predicting drug like molecules.
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Biology Direct publishes in the following sections:
- Evolutionary Biology
- Mathematical Biology
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- Structural & Molecular biology
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Edited by Dr Maureen O'Malley and Dr Yan Boucher
Published: 30 June 2011
Edited by Prof Marek Kimmel
Published: 20 April 2010
Edited by Dr Eugene Koonin
Published: 24 April 2009
Edited by Dr Eugene Koonin
Published: 9 July 2008
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