Abstract:
BACKGROUND:The accurate determination of the genomic coordinates for a given gene - its gene model - is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently-available methods of computational gene prediction, while on the whole successful, frequently disagree on the model for a given predicted gene, with some or all of the variant gene models often failing to match the biologically observed structure. Many prediction methods can be bolstered by using experimental data such as RNA-seq. However, these resources are not always available, and rarely give a comprehensive portrait of an organism's transcriptome due to temporal and tissue-specific expression profiles. RESULTS:Orthology between genes provides evolutionary evidence to guide the construction of gene models. OMGene (Optimise My Gene) aims to improve gene model accuracy in the absence of experimental data by optimising the consistency of multiple sequence alignments of orthologous genes from multiple species. Using RNA-seq data sets from plants, mammals, and fungi, considering intron/exon junction representation and exon coverage, and assessing the intra-orthogroup consistency of subcellular localisation predictions, we demonstrate the utility of OMGene for improving gene models in annotated genomes. CONCLUSIONS:We show that significant improvements in the accuracy of gene model annotations can be made, both in established and in de novo annotated genomes, by leveraging information from multiple species.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Dunne MP,Kelly Sdoi
10.1186/s12864-018-4704-zsubject
Has Abstractpub_date
2018-04-27 00:00:00pages
307issue
1issn
1471-2164pii
10.1186/s12864-018-4704-zjournal_volume
19pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The spiral cleavage mode of early development is utilized in over one-third of all animal phyla and generates embryonic cells of different size, position, and fate through a conserved set of stereotypic and invariant asymmetric cell divisions. Despite the widespread use of spiral cleavage, regulatory and mol...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2860-6
更新日期:2016-08-05 00:00:00
abstract:BACKGROUND:Evolution of novel protein-coding genes is the bedrock of adaptive evolution. Recently, we identified six protein-coding genes with similar signal sequence from Schistosoma japonicum egg stage mRNA using signal sequence trap (SST). To find the mechanism underlying the origination of these genes with similar ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-260
更新日期:2012-06-20 00:00:00
abstract:BACKGROUND:Essential genes are indispensable for the survival of living entities. They are the cornerstones of synthetic biology, and are potential candidate targets for antimicrobial and vaccine design. DESCRIPTION:Here we describe the Cluster of Essential Genes (CEG) database, which contains clusters of orthologous ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-769
更新日期:2013-11-09 00:00:00
abstract:BACKGROUND:Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06955-7
更新日期:2020-08-14 00:00:00
abstract:BACKGROUND:Chloroplasts have their own genomes, independent from nuclear genomes, that play vital roles in growth, which is a major targeted trait for genetic improvement in Populus. Angiosperm chloroplast genomes are maternally inherited, but the chloroplast' variation pattern of poplar at the single-base level during...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4813-8
更新日期:2018-05-29 00:00:00
abstract:BACKGROUND:Mapping DNaseI hypersensitive sites is commonly used to identify regulatory regions in the genome. However, currently available methods are either time consuming and laborious, expensive or require large numbers of cells. We aimed to develop a quick and straightforward method for the analysis of DNaseI hyper...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-412
更新日期:2009-09-04 00:00:00
abstract:BACKGROUND:Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors upon radiotherapy decrease according to the sizes of tumors and RT models based on Poisson statistics ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S2-S9
更新日期:2008-09-16 00:00:00
abstract:BACKGROUND:Aspartic proteases are known to play an important role in the biology of nematode parasitism. This role is best characterised in blood-feeding nematodes, where they digest haemoglobin, but they are also likely to play important roles in the biology of nematode parasites that do not feed on blood. In the pres...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-611
更新日期:2009-12-16 00:00:00
abstract:BACKGROUND:The siRNA and piRNA pathways have been shown in insects to be essential for regulation of gene expression and defence against exogenous and endogenous genetic elements (viruses and transposable elements). The vast majority of endogenous small RNAs produced by the siRNA and piRNA pathways originate from repet...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1436-1
更新日期:2015-04-10 00:00:00
abstract:BACKGROUND:Fasting induces specific molecular and metabolic adaptions in most organisms. In biomedical research fasting is used in metabolic studies to synchronize nutritional states of study subjects. Because there is a lack of standardization for this procedure, we need a deeper understanding of the dynamics and the ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-758
更新日期:2013-11-05 00:00:00
abstract:BACKGROUND:Tumor necrosis factor alpha (TNF) is able to induce a variety of biological responses in the nervous system including inflammation and neuroprotection. Human astrocytoma cells U373 have been widely used as a model for inflammatory cytokine actions in the nervous system. Here we used cDNA microarrays to analy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-4-46
更新日期:2003-11-25 00:00:00
abstract:BACKGROUND:RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological vari...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-252
更新日期:2006-10-09 00:00:00
abstract:BACKGROUND:The unfolded protein response (UPR) is a network of intracellular signaling pathways that supports the ability of the secretory pathway to maintain a balance between the load of proteins entering the endoplasmic reticulum (ER) and the protein folding capacity of the ER lumen. Current evidence indicates that ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-159
更新日期:2014-02-25 00:00:00
abstract:BACKGROUND:Numerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates. RESULTS:To enable functional analysis of human transposase-derived genes, we comb...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2877-x
更新日期:2016-08-04 00:00:00
abstract:BACKGROUND:Paired-tag sequencing approaches are commonly used for the analysis of genome structure. However, mammalian genomes have a complex organization with a variety of repetitive elements that complicate comprehensive genome-wide analyses. RESULTS:Here, we systematically assessed the utility of paired-end and mat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-257
更新日期:2013-04-16 00:00:00
abstract:BACKGROUND:DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not been explored. RESULTS:To investigate the occurrence of DNA methylation changes in LTP, we undertook ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3621-x
更新日期:2017-03-23 00:00:00
abstract:BACKGROUND:In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-325
更新日期:2011-06-23 00:00:00
abstract:BACKGROUND:Sorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-356
更新日期:2011-07-08 00:00:00
abstract:BACKGROUND:In the postgenome era, a prediction of response to treatment could lead to better dose selection for patients in radiotherapy. To identify a radiosensitive gene signature and elucidate related signaling pathways, four different microarray experiments were reanalyzed before radiotherapy. RESULTS:Radiosensiti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-348
更新日期:2012-07-30 00:00:00
abstract:BACKGROUND:Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the mainte...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-740
更新日期:2013-10-29 00:00:00
abstract:BACKGROUND:Streptococcus agalactiae (group B Streptococcus; GBS) is a significant bacterial pathogen of neonates and an emerging pathogen of adults. Though transcriptional regulators are abundantly encoded on the GBS genome, their role in GBS pathogenesis is poorly understood. The mtaR gene encodes a putative LysR-type...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-607
更新日期:2008-12-16 00:00:00
abstract:BACKGROUND:Arsenic (As) exposure is a significant worldwide environmental health concern. Low dose, chronic arsenic exposure has been associated with a higher than normal risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes. While arsenic-induced biological changes play a role in disea...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1295-9
更新日期:2015-03-19 00:00:00
abstract:BACKGROUND:Fusion genes are known to be drivers of many common cancers, so they are potential markers for diagnosis, prognosis or therapy response. The advent of paired-end RNA sequencing enhances our ability to discover fusion genes. While there are available methods, routine analyses of large number of samples are st...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5156-1
更新日期:2018-11-01 00:00:00
abstract:BACKGROUND:Restriction-modification (R-M) systems protect bacteria and archaea from attacks by bacteriophages and archaeal viruses. An R-M system specifically recognizes short sites in foreign DNA and cleaves it, while such sites in the host DNA are protected by methylation. Prokaryotic viruses have developed a number ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5324-3
更新日期:2018-12-07 00:00:00
abstract:BACKGROUND:Calcium-dependent protein kinase (CPK) is one of the main Ca2+ combined protein kinase that play significant roles in plant growth, development and response to multiple stresses. Despite an important member of the stress responsive gene family, little is known about the evolutionary history and expression pa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6501-8
更新日期:2020-01-23 00:00:00
abstract:BACKGROUND:In most species of mammals, the TRB locus has the common feature of a library of TRBV genes positioned at the 5'- end of two in tandem aligned D-J-C gene clusters, each composed of a single TRBD gene, 6-7 TRBJ genes and one TRBC gene. An enhancer located at the 3'end of the last TRBC and a well-defined promo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-3
更新日期:2010-01-04 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are a large family of endogenous, non-coding RNAs, about 22 nucleotides long, which regulate gene expression through sequence-specific base pairing with target mRNAs. Extensive studies have shown that miRNA expression in the skin changes remarkably during distinct stages of the hair cycle ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-511
更新日期:2013-07-28 00:00:00
abstract:BACKGROUND:Aberrant DNA methylation is a hallmark of many cancers. Classically there are two types of endometrial cancer, endometrioid adenocarcinoma (EAC), or Type I, and uterine papillary serous carcinoma (UPSC), or Type II. However, the whole genome DNA methylation changes in these two classical types of endometrial...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-868
更新日期:2014-10-06 00:00:00
abstract:BACKGROUND:The recent advances in next generation sequencing technology have made the sequencing of RNA (i.e., RNA-Seq) an extemely popular approach for gene expression analysis. Identification of significant differential expression represents a crucial initial step in these analyses, on which most subsequent inference...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2848-2
更新日期:2016-08-04 00:00:00
abstract:BACKGROUND:The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also unc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6123-1
更新日期:2019-10-23 00:00:00