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 fairly divergent sequences such as human and mouse genomic sequences. It consists of several efficient components: bit-level coding, search for matching segments between the two sequences as alignment anchors, longest increasing subsequence (LIS), and optimal local alignment. Efforts have been made to reduce the execution time of the program to make it truly practical for aligning very long sequences. Empirical tests suggest that for relatively divergent sequences such as sequences from different mammalian orders or from a mammal and a nonmammalian vertebrate GS-Aligner performs better than existing methods. The program and data can be downloaded from http://pondside.uchicago.edu/~lilab/ and http://webcollab.iis.sinica.edu.tw/~biocom.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Shih AC,Li WHdoi
10.1093/molbev/msg139subject
Has Abstractpub_date
2003-08-01 00:00:00pages
1299-309issue
8eissn
0737-4038issn
1537-1719pii
msg139journal_volume
20pub_type
杂志文章abstract::We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst010
更新日期:2013-04-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026223
更新日期:2000-01-01 00:00:00
abstract::Empirical codon models (ECMs) estimated from a large number of globular protein families outperformed mechanistic codon models in their description of the general process of protein evolution. Among other factors, ECMs implicitly model the influence of amino acid properties and multiple nucleotide substitutions (MNS)....
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss266
更新日期:2013-03-01 00:00:00
abstract::Silks are strong protein fibers produced by a broad array of spiders and insects. The vast majority of known silks are large, repetitive proteins assembled into extended beta-sheet structures. Honeybees, however, have found a radically different evolutionary solution to the need for a building material. The 4 fibrous ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm171
更新日期:2007-11-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn038
更新日期:2008-05-01 00:00:00
abstract::The cellobiose catabolic system of Escherichia coli K12 is being used to study the role of cryptic genes in evolution of new functions. Escherichia coli does not use beta-glucoside sugars; however, mutations in several loci can activate the cryptic bgl operon and permit growth on the beta-glucoside sugars arbutin and ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040310
更新日期:1984-02-01 00:00:00
abstract::As the largest European herbivore, the wisent (Bison bonasus) is emblematic of the continent wildlife but has unclear origins. Here, we infer its demographic and adaptive histories from two individual whole-genome sequences via a detailed comparative analysis with bovine genomes. We estimate that the wisent and bovine...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw144
更新日期:2016-11-01 00:00:00
abstract::Multiple sequence alignment (MSA) is the heart of comparative sequence analysis. Recent studies demonstrate that MSA algorithms can produce different outcomes when analyzing genomes, including phylogenetic tree inference and the detection of adaptive evolution. These studies also suggest that the difference between MS...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss256
更新日期:2013-03-01 00:00:00
abstract::The activation peptide of mammalian trypsinogens contains a highly conserved tetra-aspartate sequence (D19-D20-D21-D22) preceding the K23-I24 scissile peptide bond, which is hydrolyzed as the first step in the activation process. Here, we examined the evolution and function of trypsinogen activation peptides through i...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg183
更新日期:2003-11-01 00:00:00
abstract::Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution-and progression-require a deep understa...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz242
更新日期:2020-02-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040199
更新日期:1995-03-01 00:00:00
abstract::Modifications to transcriptional regulators play a major role in adaptation. Here, we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase β subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adapti...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx216
更新日期:2017-11-01 00:00:00
abstract::Until recently, evolutionary questions surrounding the nature of the genetic code have been mostly limited to the realm of conjecture, modeling, and simulation due to the difficulty of altering this fundamental property of living organisms. Concerted genome and protein engineering efforts now make it possible to exper...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw094
更新日期:2016-08-01 00:00:00
abstract::Seminal fluid proteins (SFPs) mediate an array of postmating reproductive processes that influence fertilization and fertility. As such, it is widely held that SFPs may contribute to postmating, prezygotic reproductive barriers between closely related taxa. We investigated seminal fluid (SF) diversification in a recen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz235
更新日期:2020-02-01 00:00:00
abstract::The evolutionary origin of eukaryotes is a question of great interest for which many different hypotheses have been proposed. These hypotheses predict distinct patterns of evolutionary relationships for individual genes of the ancestral eukaryotic genome. The availability of numerous completely sequenced genomes cover...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst272
更新日期:2014-04-01 00:00:00
abstract::The authors of a recent manuscript in "Nature" claim to have discovered "universal trends" of amino acid gain and loss in protein evolution. Here, we show that this universal trend can be simply explained by a bias that is unavoidable with the 3-taxon trees used in the original analysis. We demonstrate that a rigorous...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl010
更新日期:2006-07-01 00:00:00
abstract::With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models ca...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi051
更新日期:2005-03-01 00:00:00
abstract::Environmental drivers of biodiversity can be identified by relating patterns of community similarity to ecological factors. Community variation has traditionally been assessed by considering changes in species composition and more recently by incorporating phylogenetic information to account for the relative similarit...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss200
更新日期:2012-12-01 00:00:00
abstract::MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)(3)), is a popular program for Bayesian inference. As a leading method of using DNA data to infer phylogeny, the (MC)(3) Bayesian algorithm and its improved and parallel versions are now not fast enough for biologists to analyze massive real-wor...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst043
更新日期:2013-06-01 00:00:00
abstract::At present there is tremendous interest in characterizing the magnitude and distribution of linkage disequilibrium (LD) throughout the human genome, which will provide the necessary foundation for genome-wide LD analyses and facilitate detailed evolutionary studies. To this end, a human high-density single-nucleotide ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg032
更新日期:2003-02-01 00:00:00
abstract::We carried out an in silico analysis of the complete genome sequences of 14 species, including eukaryotes, prokaryotes, and archaea, to investigate the proportion of amplified fragment length polymorphism bands that are homoplasious for the different species, as well as the distribution of fragment lengths. We investi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq001
更新日期:2010-05-01 00:00:00
abstract::DNA fingerprinting exhibits multilocus genotypes of individuals, detected by the use of a single multilocus probe. Consequently, population data on DNA fingerprinting do not provide a complete characterization of the genetic variation in terms of allele-frequency distributions, since neither the number of loci nor the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040086
更新日期:1994-01-01 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::Many species, including humans, have dramatically expanded their range in the past, and such range expansions had certainly an impact on their genetic diversity. For example, mutations arising in populations at the edge of a range expansion can sometimes surf on the wave of advance and thus reach a larger spatial dist...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj057
更新日期:2006-03-01 00:00:00
abstract::Based on previous observations that newly inserted LINEs and SINEs have particularly long 3' A-tails, which shorten rapidly during evolutionary time, we have analyzed the rat and mouse genomes for evidence of recently inserted SINEs and LINEs. We find that the youngest predicted subfamilies of rodent identifier (ID) e...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh225
更新日期:2004-11-01 00:00:00
abstract::Thyroid hormones are involved in the regulation of growth and metabolism in all vertebrates. Transthyretin is one of the extracellular proteins with high affinity for thyroid hormones which determine the partitioning of these hormones between extracellular compartments and intracellular lipids. During vertebrate evolu...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026403
更新日期:2000-08-01 00:00:00
abstract::Parasites sometimes expand their host range by acquiring a new host species. After a host change event, the selective regime acting on a given parasite gene may change as a result of host-specific adaptive alterations of protein functionality or host-specific immune-mediated selection. We present a codon-based model t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg149
更新日期:2003-08-01 00:00:00
abstract::Gene orders have been shown to be generally unstable by comprehensive analyses in several complete genomes. In this study, we examined instability of genome structures within operons, where functionally related genes are clustered. We compared gene orders of known operons obtained from Escherichia coli and Bacillus su...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026114
更新日期:1999-03-01 00:00:00
abstract::Multilocus sequence typing (MLST) is a recently developed nucleotide sequence-based method for the definitive assignment of isolates within bacterial populations to specific clones. MLST uses the same principles as multilocus enzyme electrophoresis and provides data that can be used to investigate aspects of the popul...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026061
更新日期:1999-11-01 00:00:00
abstract::Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy074
更新日期:2018-06-01 00:00:00