Abstract:
BACKGROUND:Genomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes. RESULTS:We have analyzed aspects of the information content of Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, and Escherichia coli (K-12) genomes. Virtually all possible (> 98%) 12 bp oligomers appear in vertebrate genomes while < 2% of 19 bp oligomers are present. Other species showed different ranges of > 98% to < 2% of possible oligomers in D. melanogaster (12-17 bp), C. elegans (11-17 bp), A. thaliana (11-17 bp), S. cerevisiae (10-16 bp) and E. coli (9-15 bp). Frequencies of unique oligomers in the genomes follow similar patterns. We identified a set of 2.6 M 15-mers that are more than 1 nucleotide different from all 15-mers in the human genome and so could be used as probes to detect microbes in human samples. In a human sample, these probes would detect 100% of the 433 currently fully sequenced prokaryotes and 75% of the 3065 fully sequenced viruses. The human genome is significantly more compact in sequence space than a random genome. We identified the most frequent 5- to 20-mers in the human genome, which may prove useful as PCR primers. We also identified a bacterium, Anaeromyxobacter dehalogenans, which has an exceptionally low diversity of oligomers given the size of its genome and its GC content. The entropy of coding regions in the human genome is significantly higher than non-coding regions and chromosomes. However chromosomes 1, 2, 9, 12 and 14 have a relatively high proportion of coding DNA without high entropy, and chromosome 20 is the opposite with a low frequency of coding regions but relatively high entropy. CONCLUSION:Measures of the frequency of oligomers are useful for designing PCR assays and for identifying chromosomes and organisms with hidden structure that had not been previously recognized. This information may be used to detect novel microbes in human tissues.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Liu Z,Venkatesh SS,Maley CCdoi
10.1186/1471-2164-9-509subject
Has Abstractpub_date
2008-10-30 00:00:00pages
509issn
1471-2164pii
1471-2164-9-509journal_volume
9pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-150
更新日期:2010-03-04 00:00:00
abstract:BACKGROUND:HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-156
更新日期:2006-06-17 00:00:00
abstract:BACKGROUND:Brain and immune system are linked in a bi-directional manner. To date, it remained largely unknown why immune components become suppressed, enhanced, or remain unaffected in relation to psychosocial stress. Therefore, we mixed unfamiliar pigs with different levels of aggressiveness. We separated castrated m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-967
更新日期:2014-11-08 00:00:00
abstract:BACKGROUND:Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immun...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5362-x
更新日期:2019-01-05 00:00:00
abstract:BACKGROUND:Dimension reduction is a critical issue in the analysis of microarray data, because the high dimensionality of gene expression microarray data set hurts generalization performance of classifiers. It consists of two types of methods, i.e. feature selection and feature extraction. Principle component analysis ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S2-S24
更新日期:2008-09-16 00:00:00
abstract::The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the billions of base-pairs of Archosaur sequence that have become available in the last few years. This editorial de...
journal_title:BMC genomics
pub_type:
doi:10.1186/1471-2164-10-S2-I1
更新日期:2009-07-14 00:00:00
abstract:BACKGROUND:Transmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IP...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6156-5
更新日期:2019-11-04 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known to be associated with disease phenotypes and to display tissue-specific patterns of expression. ME...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3114-3
更新日期:2016-10-04 00:00:00
abstract:BACKGROUND:Compromised intestinal barrier (CIB) has been associated with many enteropathies, including colorectal cancer (CRC) and inflammatory bowel disease (IBD). We hypothesized that CIB could lead to increased host-derived contents including epithelial cells into the gut, change its physio-metabolic properties, and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6749-z
更新日期:2020-05-11 00:00:00
abstract:BACKGROUND:Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2474-z
更新日期:2016-02-29 00:00:00
abstract:BACKGROUND:The bulldog calf syndrome is a lethal form of the inherited congenital chondrodysplasias. Among the progeny of the polled Holstein bull Energy P cases of lethal chondrodysplasia were observed. Pedigrees of the cases and the frequency of 3/8 cases among the offspring of Energy P at our teaching and experiment...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4153-0
更新日期:2017-10-10 00:00:00
abstract:BACKGROUND:Parasitic wasps constitute one of the largest group of venomous animals. Although some physiological effects of their venoms are well documented, relatively little is known at the molecular level on the protein composition of these secretions. To identify the majority of the venom proteins of the endoparasit...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-693
更新日期:2010-12-07 00:00:00
abstract:BACKGROUND:The ability to rapidly map millions of oligonucleotide fragments to a reference genome is crucial to many high throughput genomic technologies. RESULTS:We propose an intuitive and efficient algorithm, titled extreme MApping of OligoNucleotide (xMAN), to rapidly map millions of oligonucleotide fragments to a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S1-S20
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:The pattern of point mutation is important for studying mutational mechanisms, genome evolution, and diseases. Previous studies of mutation direction were largely based on substitution data from a limited number of loci. To date, there is no genome-wide analysis of mutation direction or methylation-dependent...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-316
更新日期:2006-12-13 00:00:00
abstract:BACKGROUND:Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) hav...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2031-1
更新日期:2015-10-13 00:00:00
abstract:BACKGROUND:Embryonic and fetal exposure to maternal obesity causes several maladaptive morphological and epigenetic changes in exposed offspring. The timing of these events is unclear, but changes can be observed even after a short exposure to maternal obesity around the time of conception. The hypothesis of this work ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5120-0
更新日期:2018-10-11 00:00:00
abstract:BACKGROUND:Precise identification of three-dimensional genome organization, especially enhancer-promoter interactions (EPIs), is important to deciphering gene regulation, cell differentiation and disease mechanisms. Currently, it is a challenging task to distinguish true interactions from other nearby non-interacting o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4459-6
更新日期:2018-05-09 00:00:00
abstract:BACKGROUND:Lysophosphatidic acid acyltransferase (LPAAT) encoded by a multigene family is a rate-limiting enzyme in the Kennedy pathway in higher plants. Cotton is the most important natural fiber crop and one of the most important oilseed crops. However, little is known on genes coding for LPAATs involved in oil biosy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3594-9
更新日期:2017-03-01 00:00:00
abstract:BACKGROUND:The principal toxicity of acute organophosphate (OP) pesticide poisoning is the disruption of neurotransmission through inhibition of acetylcholinesterase (AChE). However, other mechanisms leading to persistent effects and neurodegeneration remain controversial and difficult to detect. Because Caenorhabditis...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-291
更新日期:2013-04-30 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initiation and progression of cancer. Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3238-5
更新日期:2016-11-08 00:00:00
abstract:BACKGROUND:The regenerative response of Schwann cells after peripheral nerve injury is a critical process directly related to the pathophysiology of a number of neurodegenerative diseases. This SC injury response is dependent on an intricate gene regulatory program coordinated by a number of transcription factors and m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-84
更新日期:2013-02-06 00:00:00
abstract:BACKGROUND:Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1(CA) oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecula...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-182
更新日期:2014-03-09 00:00:00
abstract:BACKGROUND:Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT). RESULTS:We analyzed the postnatal transformation of adipose in sheep with a time course study of the ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1405-8
更新日期:2015-03-19 00:00:00
abstract:BACKGROUND:Co-expressing genes tend to cluster in eukaryotic genomes. This paper analyzes correlation between the proximity of eukaryotic genes and their transcriptional expression pattern in the zebrafish (Danio rerio) genome using available microarray data and gene annotation. RESULTS:The analyses show that neighbou...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-42
更新日期:2009-01-22 00:00:00
abstract:BACKGROUND:A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the genomic variants of complex traits might be enriched in a subset of genomic regions defined by genes gro...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4004-z
更新日期:2017-08-10 00:00:00
abstract:BACKGROUND:The Xanthomonas citri pv. citri (X. citri) is a phytopathogenic bacterium that infects different species of citrus plants where it causes canker disease. The adaptation to different habitats is related to the ability of the cells to metabolize and to assimilate diverse compounds, including sulfur, an essenti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1736-5
更新日期:2015-07-14 00:00:00
abstract:BACKGROUND:Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-637
更新日期:2008-12-31 00:00:00
abstract:BACKGROUND:Nontuberculous mycobacterium (NTM) species are ubiquitous microorganisms. NTM pulmonary disease (NTM-PD) is thought to be caused not by human-to-human transmission but by independent environmental acquisition. However, recent studies using next-generation sequencing (NGS) have reported trans-continental spre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6738-2
更新日期:2020-04-23 00:00:00
abstract:BACKGROUND:Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-347
更新日期:2013-05-24 00:00:00
abstract:BACKGROUND:Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs) map each mutant to a specific locus within the genome. In maize, FSTs have...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-116
更新日期:2007-05-09 00:00:00