Motivation: The rapidly growing number of available prokaryotic genome sequences requires fully automated and high-quality software solutions for their initial and re-annotation. Here we present ConsPred, a prokaryoti...
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Motivation: The rapidly growing number of available prokaryotic genome sequences requires fully automated and high-quality software solutions for their initial and re-annotation. Here we present ConsPred, a prokaryotic genome annotation framework that performs intrinsic gene predictions, homology searches, predictions of non-coding genes as well as CRISPR repeats and integrates all evidence into a consensus annotation. ConsPred achieves comprehensive, high-quality annotations based on rules and priorities, similar to decision-making in manual curation and avoids conflicting predictions. Parameters controlling the annotation process are configurable by the user. ConsPred has been used in the institutions of the authors for longer than 5 years and can easily be extended and adapted to specific needs. Summary:The ConsPred algorithm for producing a consensus from the varying scores of multiple gene prediction programs approaches manual curation in accuracy. Its rule-based approach for choosing final predictions avoids overriding previous manual curations.
For sufficiently long genomic sequence, the frequency of any short nucleotide fragment on one strand is approximately equal to the frequency of its reverse complement on the same strand. Despite being studied over two...
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For sufficiently long genomic sequence, the frequency of any short nucleotide fragment on one strand is approximately equal to the frequency of its reverse complement on the same strand. Despite being studied over two decades, the precise mechanism involved has not yet been made clear. In this study, we calculated the high order intra-strand partial symmetry (IPS) for 14 animal species by using a fixed sliding window method to scan each genome sequence. The study showed that the IPS was positive associated with organismal complexity measured by the number of distinct cell types. The results indicated that the IPS might be resulted from the increasing of functional non-coding dnas, and plays an important role in the evolution process of complex body plans.
Within-intron difference of correlation with base composition of the adjacent exons was studied in the genomes of 34 species. For this purpose, GC-percent was determined for segments of 50 bp in length taken at both i...
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Within-intron difference of correlation with base composition of the adjacent exons was studied in the genomes of 34 species. For this purpose, GC-percent was determined for segments of 50 bp in length taken at both intron margins and in the internal part of the intron. It was found that in certain genomes the coefficient of correlation with GC-percent of the adjacent exon was significantly higher for the intron margin than for the internal part of the intron (homeotherms, cereals,). Only part of this difference can be explained by unequal probability of insertion of transposable elements. Those multicellular organisms which have a low or no within-intron difference in correlation with the adjacent exons (anamniotes, invertebrates, dicots) show a higher local compositional heterogeneity (a greater exon/intron contrast in the GC-content). These results are evidence against the mutational bias being a possible explanation for the compositional genome heterogeneity. Thus, in the genomes with a high global heterogeneity there seems to be a selective force for compliance of intron base composition with the adjacent exons. This force is stronger in those parts of the intron that are closer to exons. In addition, the previously found positive general correlation between the genome size and average intron length was confirmed with a much larger dataset. However, within separate phylogenetic groups this rule can be broken, as it occurs in the cereals (family Poaceae), where a negative correlation was found. (C) 2001 Published by Elsevier Science B.V.
The importance of statistical patterns of language has been debated over decades. Although Zipf's law is perhaps the most popular case, recently, Menzerath's law has begun to be involved. Menzerath's law m...
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The importance of statistical patterns of language has been debated over decades. Although Zipf's law is perhaps the most popular case, recently, Menzerath's law has begun to be involved. Menzerath's law manifests in language, music and genomes as a tendency of the mean size of the parts to decrease as the number of parts increases in many situations. This statistical regularity emerges also in the context of genomes, for instance, as a tendency of species with more chromosomes to have a smaller mean chromosome size. It has been argued that the instantiation of this law in genomes is not indicative of any parallel between language and genomes because (a) the law is inevitable and (b) noncodingdna dominates genomes. Here mathematical, statistical, and conceptual challenges of these criticisms are discussed. Two major conclusions are drawn: the law is not inevitable and languages also have a correlate of noncodingdna. However, the wide range of manifestations of the law in and outside genomes suggests that the striking similarities between noncodingdna and certain linguistics units could be anecdotal for understanding the recurrence of that statistical law. (c) 2012 Wiley Periodicals, Inc. Complexity, 2012
The article reports that noncoding RNAs precisely regulate the messenger RNA (mRNA) profile in platelets. It states how interfering in this process using genetically engineered mice affects hemostatic and thrombotic f...
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The article reports that noncoding RNAs precisely regulate the messenger RNA (mRNA) profile in platelets. It states how interfering in this process using genetically engineered mice affects hemostatic and thrombotic functions of platelets. The reduction of miRNA expression in the absence of Dicer1 is reported to suggest that the miRNAs are mainly generated before PF4 activation, highlighting the stability of miRNA in maturing megakaryocytes and platelets.
The gene encoding the androgen receptor (AR) is associated with male pattern baldness (androgenetic alopecia - AGA). In case-control and family analyses, we mapped AR and the adjacent intergenic regions. We found evid...
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The gene encoding the androgen receptor (AR) is associated with male pattern baldness (androgenetic alopecia - AGA). In case-control and family analyses, we mapped AR and the adjacent intergenic regions. We found evidence for association with two independent loci, one upstream and previously described and the other downstream and apparently novel. The haplotype comprising these SNPs was strongly associated with AGA (P = 3.75 x 10-5) in 1195 men. We also replicated association with a recently reported non-coding region on chromosome 20 and found that its association with AGA was less strong and independent of that of AR. Our results will help focus future efforts to further define AGA genetic risk.
Humans vary according to a plethora of traits, such as height, hair color, behavior, and susceptibility to disease. Both genetics (nature) and environment (nurture) contribute to this variation. Recent large-scale gen...
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Humans vary according to a plethora of traits, such as height, hair color, behavior, and susceptibility to disease. Both genetics (nature) and environment (nurture) contribute to this variation. Recent large-scale genetic studies have identified thousands of specific dna variations in the human population that are associated with different traits. However, these studies do not answer a key question: By what means do most dna variants alter cellular behavior and contribute to differences in specific traits, such as height? A trio of papers in this issue by Kasowski et al. on page 750 (1), Kilpinen et al. on page 744 (2), and McVicker et al. on page 747 (3) provide a framework for exploring the mechanistic link between genetic and trait variation in the human population. Specifically, they find that dna variants influence a layer of gene regulation called epigenetics through the sequence-specific activity of transcription factors.
MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been develo...
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MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods. Here, we present tools4miRs, the first platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can additionally filter the available methods according to their specific research needs, capabilities and preferences. Tools4miRs is also a web-based target prediction meta-server that incorporates user-designated target prediction methods into the analysis of user-provided data.
A major challenge in human genetics is pinpointing which non-coding genetic variants affect gene expression and disease risk. A new study in this issue describes a broadly applicable approach for this task that explic...
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A major challenge in human genetics is pinpointing which non-coding genetic variants affect gene expression and disease risk. A new study in this issue describes a broadly applicable approach for this task that explicitly models cell type-specific regulatory motifs and generates variant effect predictions that are more accurate and interpretable than those of alternative tools.
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