Abstract:
:Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Priyam A,Woodcroft BJ,Rai V,Moghul I,Munagala A,Ter F,Chowdhary H,Pieniak I,Maynard LJ,Gibbins MA,Moon H,Davis-Richardson A,Uludag M,Watson-Haigh NS,Challis R,Nakamura H,Favreau E,Gómez EA,Pluskal T,Leonard G,Rumpdoi
10.1093/molbev/msz185subject
Has Abstractpub_date
2019-12-01 00:00:00pages
2922-2924issue
12eissn
0737-4038issn
1537-1719pii
5549819journal_volume
36pub_type
杂志文章abstract::Successful fertilization in free-spawning marine organisms depends on the interactions between genes expressed on the surfaces of eggs and sperm. Positive selection frequently characterizes the molecular evolution of such genes, raising the possibility that some common deterministic process drives the evolution of gam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl062
更新日期:2006-10-01 00:00:00
abstract::Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa283
更新日期:2020-11-03 00:00:00
abstract::Single-stranded DNA(ssDNA) viral life cycles must balance double-stranded DNA (dsDNA) and ssDNA biosynthesis. Previously published in vitro results suggest that microvirus C and host cell SSB proteins play antagonistic roles to achieve this balance. To investigate this in vivo, microvirus DNA replication was character...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu089
更新日期:2014-06-01 00:00:00
abstract::Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patter...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv346
更新日期:2016-04-01 00:00:00
abstract::The phylogenies for each of the protein-coding genes from the Methanococcus jannaschii genome were surveyed to determine the history of the major groups of life. For each gene, homologous sequences from other archaea, eucarya, and Gram-positive and Gram-negative bacteria were collected and aligned, and a phylogeny was...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025983
更新日期:1998-07-01 00:00:00
abstract::Copy number variants (CNVs) within humans can have both adaptive and deleterious effects. Because of their phenotypic significance, researchers have attempted to find single nucleotide polymorphisms (SNPs) in high linkage disequilibrium (LD) with CNVs to use in genomewide association studies. However, studies have fou...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp210
更新日期:2010-01-01 00:00:00
abstract::Malaria is a deadly disease that causes nearly one million deaths each year. To develop methods to control and eradicate malaria, it is important to understand the genetic basis of Plasmodium falciparum adaptations to antimalarial treatments and the human immune system while taking into account its demographic history...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss161
更新日期:2012-11-01 00:00:00
abstract::We examined microsatellite variation in two diploid, outcrossing relatives of Arabidopsis thaliana, Arabis petraea and Arabis lyrata. The primer sequences were derived from A. thaliana. About 50% (14 loci) of the A. thaliana primers could successfully amplify microsatellites in the related species. Analysis of microsa...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025758
更新日期:1997-03-01 00:00:00
abstract::The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon lncRNA perturbation, key biological roles were demonstrated for ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz212
更新日期:2020-01-01 00:00:00
abstract::Male reproductive fitness is strongly affected by seminal fluid. In addition to interacting with the female environment, seminal fluid mediates important physiological characteristics of sperm, including capacitation and motility. In mammals, the male reproductive tract shows a striking degree of compartmentalization,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp094
更新日期:2009-08-01 00:00:00
abstract::Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrop...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040333
更新日期:1985-01-01 00:00:00
abstract::Random genetic drift, or stochastic change in gene frequency, is a fundamental evolutionary force that is usually defined within the ideal Wright-Fisher (WF) population. However, as the theory is increasingly applied to populations that deviate strongly from the ideal model, a paradox of random drift has emerged. When...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx161
更新日期:2017-08-01 00:00:00
abstract::The RIIIS/J inbred mouse strain is a model for type 1 von Willebrand disease (VWD), a common human bleeding disorder. Low von Willebrand factor (VWF) levels in RIIIS/J are due to a regulatory mutation, Mvwf1, which directs a tissue-specific switch in expression of a glycosyltransferase, B4GALNT2, from intestine to blo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn284
更新日期:2009-03-01 00:00:00
abstract::Subspecies nomenclature systems of pathogens are increasingly based on sequence data. The use of phylogenetics to identify and differentiate between clusters of genetically similar pathogens is particularly prevalent in virology from the nomenclature of human papillomaviruses to highly pathogenic avian influenza (HPAI...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz053
更新日期:2019-07-01 00:00:00
abstract::Endogenous retroviruses are ubiquitous in the vertebrate genomes. On occasion, hosts recruited retroviral genes to mediate their own biological functions, a process formally known as co-option or exaptation. Much remains unknown about the extent of retroviral gene co-option in vertebrates, although more than ten retro...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa180
更新日期:2020-11-01 00:00:00
abstract::The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such except...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz294
更新日期:2020-04-01 00:00:00
abstract::Although endogenous retroviruses are common across vertebrate genomes, the koala retrovirus (KoRV) is the only retrovirus known to be currently invading the germ line of its host. KoRV is believed to have first infected koalas in northern Australia less than two centuries ago. We examined KoRV in 28 koala museum skins...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss223
更新日期:2013-02-01 00:00:00
abstract::The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp278
更新日期:2010-03-01 00:00:00
abstract::Despite the importance of plant-plant interactions on plant community dynamics and crop yield, our understanding of the adaptive genetics underlying these interactions is still limited and deserves to be investigated in the context of complex and diffuse interactions occurring in plant assemblages. Here, based on 145 ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz078
更新日期:2019-07-01 00:00:00
abstract::Detecting selection on codon usage (CU) is a difficult task, since CU can be shaped by both the mutational process and selective constraints operating at the DNA, RNA, and protein levels. Yang and Nielsen (2008) developed a test (which we call CUYN) for detecting selection on CU using two competing mutation-selection ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy047
更新日期:2018-06-01 00:00:00
abstract::Previous studies have shown that genes that are expressed predominantly or exclusively in males tend to evolve rapidly in comparison to other genes. In most cases, however, it is unknown whether this rapid evolution is the result of increased positive (or sexual) selection on male-expressed traits or if it is due to a...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msi189
更新日期:2005-10-01 00:00:00
abstract::MicroRNA (miRNA) sponges are vital components of posttranscriptional gene regulation. Yet, only a limited number of miRNA sponges have been identified. Here, we show that the recently evolved noncoding tumor suppressor transcript, antisense RNA to TP73 gene (TP73-AS1), functions as a natural sponge of human-specific m...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy022
更新日期:2018-05-01 00:00:00
abstract::The degree to which an amino acid site is free to vary is strongly dependent on its structural and functional importance. An amino acid that plays an essential role is unlikely to change over evolutionary time. Hence, the evolutionary rate at an amino acid site is indicative of how conserved this site is and, in turn,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh194
更新日期:2004-09-01 00:00:00
abstract::Protein tyrosine phosphorylation is a key regulatory modification in metazoans, and the corresponding kinase enzymes have diversified dramatically. This diversification is correlated with a genome-wide reduction in protein tyrosine content, and it was recently suggested that this reduction was driven by selection to a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu284
更新日期:2015-01-01 00:00:00
abstract::In phylogenetic inference, an evolutionary model describes the substitution processes along each edge of a phylogenetic tree. Misspecification of the model has important implications for the analysis of phylogenetic data. Conventionally, however, the selection of a suitable evolutionary model is based on heuristics or...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr259
更新日期:2012-03-01 00:00:00
abstract::A novel algorithm, GS-Aligner, that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg139
更新日期:2003-08-01 00:00:00
abstract::Sequencing multiple copies of the ITS1 region revealed the coexistence of two or more haplotypes within the genome of Chorthippus parallelus. Using a PCR-RFLP approach, the ITS1 numbers and frequencies of haplotypes present in each of 40 individuals were investigated, revealing a consistent lack of homogeneity. For ea...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh163
更新日期:2004-08-01 00:00:00
abstract::Phylogenetic analyses of closely related species should use information from multiple, independent genes with relatively high rates of sequence evolution. To investigate species for which there are few prior sequence data for single-copy nuclear (scnDNA) genes, primers for gene amplification can be designed to highly ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040117
更新日期:1994-05-01 00:00:00
abstract::A major limitation on ability to reconstruct bacterial evolution is the lack of dated ancestors that might be used to evaluate and calibrate molecular clocks. Vertically transmitted symbionts that have cospeciated with animal hosts offer a firm basis for calibrating sequence evolution in bacteria, since fossils of the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026071
更新日期:1999-11-01 00:00:00
abstract::Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprin...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025728
更新日期:1997-12-01 00:00:00