Abstract:
BACKGROUND:The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. RESULTS:We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. CONCLUSIONS:CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Liu C,Shi L,Zhu Y,Chen H,Zhang J,Lin X,Guan Xdoi
10.1186/1471-2164-13-715subject
Has Abstractpub_date
2012-12-20 00:00:00pages
715issn
1471-2164pii
1471-2164-13-715journal_volume
13pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Bombyx mori was domesticated from the Chinese wild silkworm, Bombyx mandarina. Wild and domestic silkworms are good models in which to investigate genes related to silk protein synthesis that may be differentially expressed in silk glands, because their silk productions are very different. Here we used the m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1287-9
更新日期:2015-02-06 00:00:00
abstract:BACKGROUND:Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-326
更新日期:2011-06-23 00:00:00
abstract:BACKGROUND:Meta-analysis of QTLs combines the results of several QTL detection studies and provides narrow confidence intervals for meta-QTLs, permitting easier positional candidate gene identification. It is usually applied to multiple mapping populations, but can be applied to one. Here, a meta-analysis of drought re...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-10-276
更新日期:2009-06-22 00:00:00
abstract:BACKGROUND:Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. RESULTS:We have used array comparative genomic hybridization (aCGH)...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-62
更新日期:2010-01-25 00:00:00
abstract:BACKGROUND:Repetitive DNA is a major component of plant genomes and is thought to be a driver of evolutionary novelty. Describing variation in repeat content among individuals and between populations is key to elucidating the evolutionary significance of repetitive DNA. However, the cost of producing references genomes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6517-0
更新日期:2020-01-30 00:00:00
abstract:BACKGROUND:There is interest in improving the flavor of commercial strawberry (Fragaria × ananassa) varieties. Fruit flavor is shaped by combinations of sugars, acids and volatile compounds. Many efforts seek to use genomics-based strategies to identify genes controlling flavor, and then designing durable molecular mar...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-217
更新日期:2014-04-17 00:00:00
abstract:BACKGROUND:The variability in gene organization and architecture of green algal mitochondrial genomes is only recently being studied on a finer taxonomic scale. Sequenced mt genomes from the chlorophycean orders Volvocales and Sphaeropleales exhibit considerable variation in size, content, and structure, even among clo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2056-5
更新日期:2015-10-21 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:The use of dispersants can be an effective way to deal with acute oil spills to limit environmental damage, however very little is known about whether chemically dispersed oil have the same toxic effect on marine organisms as mechanically dispersed oil. We exposed Atlantic cod larvae to chemically and mechan...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-702
更新日期:2012-12-14 00:00:00
abstract:BACKGROUND:ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4559-3
更新日期:2018-03-01 00:00:00
abstract:BACKGROUND:The emergence of epithelia was the foundation of metazoan expansion. Epithelial tissues are a hallmark of metazoans deeply rooted in the evolution of their complex developmental morphogenesis processes. However, studies on the epithelial features of non-bilaterians are still sparse and it remains unclear whe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4715-9
更新日期:2018-05-24 00:00:00
abstract:BACKGROUND:Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-270
更新日期:2013-04-22 00:00:00
abstract:BACKGROUND:Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnan...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-777
更新日期:2013-11-11 00:00:00
abstract:BACKGROUND:The histone variant H2A.Z, which has been reported to have both activating and repressive effects on gene expression, is known to occupy nucleosomes at the 5' ends of protein-coding genes. RESULTS:We now find that H2A.Z is also significantly enriched in gene coding regions and at the 3' ends of genes in bud...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1247-4
更新日期:2015-02-19 00:00:00
abstract:BACKGROUND:Tree peony (Paeonia suffruticosa Andrews) is a globally famous ornamental flower, with large and colorful flowers and abundant flower types. However, a relatively short and uniform flowering period hinders the applications and production of ornamental tree peony. Unfortunately, the molecular mechanism of reg...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5857-0
更新日期:2019-07-11 00:00:00
abstract::We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic var...
journal_title:BMC genomics
pub_type: 社论
doi:10.1186/s12864-017-3862-8
更新日期:2017-06-27 00:00:00
abstract:BACKGROUND:Zoysia matrella, widely used in lawns and sports fields, is of great economic and ecological value. Z. matrella is an allotetraploid species (2n = 4x = 40) in the genus zoysia under the subfamily Chloridoideae. Despite its ecological impacts and economic importance, the subfamily Chloridoideae has received l...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2969-7
更新日期:2016-08-08 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:Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6736-4
更新日期:2020-04-20 00:00:00
abstract:BACKGROUND:Mucolipidosis type IV (MLIV) is an autosomal recessive lysosomal storage disorder characterized by severe neurologic and ophthalmologic abnormalities. Recently the MLIV gene, MCOLN1, has been identified as a new member of the transient receptor potential (TRP) cation channel superfamily. Here we report the c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-3-3
更新日期:2002-01-01 00:00:00
abstract:BACKGROUND:The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-544
更新日期:2012-10-10 00:00:00
abstract:BACKGROUND:Alu repetitive elements are the abundant sequences in human genome. Diversity of DNA sequences of these elements makes difficult the construction of theoretical patterns of Alu repeats cleavage by restriction endonucleases. We have proposed a method of restriction analysis of Alu repeats sequences in silico....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-305
更新日期:2008-06-26 00:00:00
abstract:BACKGROUND:Color polymorphism in the nacre of pteriomorphian bivalves is of great interest for the pearl culture industry. The nacreous layer of the Polynesian black-lipped pearl oyster Pinctada margaritifera exhibits a large array of color variation among individuals including reflections of blue, green, yellow and pi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1776-x
更新日期:2015-08-01 00:00:00
abstract:BACKGROUND:Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-680
更新日期:2010-11-30 00:00:00
abstract:BACKGROUND:Ocean acidification (OA), a change in ocean chemistry due to the absorption of atmospheric CO2 into surface oceans, challenges biogenic calcification in many marine organisms. Ocean acidification is expected to rapidly progress in polar seas, with regions of the Southern Ocean expected to experience severe O...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4161-0
更新日期:2017-10-23 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: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:In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-646
更新日期:2013-09-23 00:00:00
abstract:BACKGROUND:The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular path...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-627
更新日期:2012-11-15 00:00:00
abstract:BACKGROUND:Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called "alpha" and "beta"-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging to alpha-rhizobia. Mimosa pudica is a legume that offers an excellent opportunity to study the adapta...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4487-2
更新日期:2018-01-30 00:00:00