Domain enhanced lookup time accelerated BLAST.

Abstract:

BACKGROUND:BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific score matrix (PSSM) for searching the database in round i + 1. Biegert and Söding developed Context-sensitive BLAST (CS-BLAST), which combines information from searching the sequence database with information derived from a library of short protein profiles to achieve better homology detection than PSI-BLAST, which builds its PSSMs from scratch. RESULTS:We describe a new method, called domain enhanced lookup time accelerated BLAST (DELTA-BLAST), which searches a database of pre-constructed PSSMs before searching a protein-sequence database, to yield better homology detection. For its PSSMs, DELTA-BLAST employs a subset of NCBI's Conserved Domain Database (CDD). On a test set derived from ASTRAL, with one round of searching, DELTA-BLAST achieves a ROC5000 of 0.270 vs. 0.116 for CS-BLAST. The performance advantage diminishes in iterated searches, but DELTA-BLAST continues to achieve better ROC scores than CS-BLAST. CONCLUSIONS:DELTA-BLAST is a useful program for the detection of remote protein homologs. It is available under the "Protein BLAST" link at http://blast.ncbi.nlm.nih.gov.

journal_name

Biol Direct

journal_title

Biology direct

authors

Boratyn GM,Schäffer AA,Agarwala R,Altschul SF,Lipman DJ,Madden TL

doi

10.1186/1745-6150-7-12

subject

Has Abstract

pub_date

2012-04-17 00:00:00

pages

12

issn

1745-6150

pii

1745-6150-7-12

journal_volume

7

pub_type

杂志文章
  • Use of designed sequences in protein structure recognition.

    abstract:BACKGROUND:Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-018-0209-6

    authors: Kumar G,Mudgal R,Srinivasan N,Sandhya S

    更新日期:2018-05-09 00:00:00

  • A network-based approach to classify the three domains of life.

    abstract:BACKGROUND:Identifying group-specific characteristics in metabolic networks can provide better insight into evolutionary developments. Here, we present an approach to classify the three domains of life using topological information about the underlying metabolic networks. These networks have been shown to share domain-...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-53

    authors: Mueller LA,Kugler KG,Netzer M,Graber A,Dehmer M

    更新日期:2011-10-13 00:00:00

  • A web server for analysis, comparison and prediction of protein ligand binding sites.

    abstract:BACKGROUND:One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. RESULTS:In order to address this problem, we developed...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-016-0118-5

    authors: Singh H,Srivastava HK,Raghava GP

    更新日期:2016-03-25 00:00:00

  • Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons.

    abstract:BACKGROUND:While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria,...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-1-28

    authors: Baranov PV,Vestergaard B,Hamelryck T,Gesteland RF,Nyborg J,Atkins JF

    更新日期:2006-09-13 00:00:00

  • Elusive data underlying debate at the prokaryote-eukaryote divide.

    abstract:BACKGROUND:The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenerge...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-018-0221-x

    authors: Gerlitz M,Knopp M,Kapust N,Xavier JC,Martin WF

    更新日期:2018-10-03 00:00:00

  • Modeling the population dynamics of lemon sharks.

    abstract:BACKGROUND:Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage these animals, more detailed treatments are often needed to assess potential drivers of population d...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-9-23

    authors: White ER,Nagy JD,Gruber SH

    更新日期:2014-11-18 00:00:00

  • Global analyses of Chromosome 17 and 18 genes of lung telocytes compared with mesenchymal stem cells, fibroblasts, alveolar type II cells, airway epithelial cells, and lymphocytes.

    abstract:BACKGROUND:Telocytes (TCs) is an interstitial cell with extremely long and thin telopodes (Tps) with thin segments (podomers) and dilations (podoms) to interact with neighboring cells. TCs have been found in different organs, while there is still a lack of TCs-specific biomarkers to distinguish TCs from the other cells...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-015-0042-0

    authors: Wang J,Ye L,Jin M,Wang X

    更新日期:2015-03-11 00:00:00

  • Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates.

    abstract:BACKGROUND:Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive families or families of repeats. Recently, we proposed that families of TEs originate in small populati...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-7-36

    authors: Jurka J,Bao W,Kojima KK,Kohany O,Yurka MG

    更新日期:2012-10-25 00:00:00

  • From tumors to species: a SCANDAL hypothesis.

    abstract::ᅟ: Some tumor cells can evolve into transmissible parasites. Notable examples include the Tasmanian devil facial tumor disease, the canine transmissible venereal tumor and transmissible cancers of mollusks. We present a hypothesis that such transmissible tumors existed in the past and that some modern animal taxa are ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-019-0233-1

    authors: Panchin AY,Aleoshin VV,Panchin YV

    更新日期:2019-01-23 00:00:00

  • The archaeo-eukaryotic GINS proteins and the archaeal primase catalytic subunit PriS share a common domain.

    abstract:UNLABELLED:Primase and GINS are essential factors for chromosomal DNA replication in eukaryotic and archaeal cells. Here we describe a previously undetected relationship between the C-terminal domain of the catalytic subunit (PriS) of archaeal primase and the B-domains of the archaeo-eukaryotic GINS proteins in the for...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-5-17

    authors: Swiatek A,Macneill SA

    更新日期:2010-04-12 00:00:00

  • Impairment of translation in neurons as a putative causative factor for autism.

    abstract:BACKGROUND:A dramatic increase in the prevalence of autism and Autistic Spectrum Disorders (ASD) has been observed over the last two decades in USA, Europe and Asia. Given the accumulating data on the possible role of translation in the etiology of ASD, we analyzed potential effects of rare synonymous substitutions ass...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-9-16

    authors: Poliakov E,Koonin EV,Rogozin IB

    更新日期:2014-07-10 00:00:00

  • The common ancestry of life.

    abstract:BACKGROUND:It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-5-64

    authors: Koonin EV,Wolf YI

    更新日期:2010-11-18 00:00:00

  • The mechanistic and evolutionary aspects of the 2'- and 3'-OH paradigm in biosynthetic machinery.

    abstract:BACKGROUND:The translation machinery underlies a multitude of biological processes within the cell. The design and implementation of the modern translation apparatus on even the simplest course of action is extremely complex, and involves different RNA and protein factors. According to the "RNA world" idea, the critica...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-8-17

    authors: Safro M,Klipcan L

    更新日期:2013-07-08 00:00:00

  • The multiple personalities of Watson and Crick strands.

    abstract:BACKGROUND:In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review t...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-7

    authors: Cartwright RA,Graur D

    更新日期:2011-02-08 00:00:00

  • The origins of phagocytosis and eukaryogenesis.

    abstract:BACKGROUND:Phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acquisition of bacterial endosymbionts including the ancestor of the mitochondrion. RESULTS:Comparisons...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-4-9

    authors: Yutin N,Wolf MY,Wolf YI,Koonin EV

    更新日期:2009-02-26 00:00:00

  • Assessment of urban microbiome assemblies with the help of targeted in silico gold standards.

    abstract:BACKGROUND:Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metageno...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-018-0225-6

    authors: Gerner SM,Rattei T,Graf AB

    更新日期:2018-10-12 00:00:00

  • IPC - Isoelectric Point Calculator.

    abstract:BACKGROUND:Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, p...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-016-0159-9

    authors: Kozlowski LP

    更新日期:2016-10-21 00:00:00

  • Orphan SelD proteins and selenium-dependent molybdenum hydroxylases.

    abstract::Bacterial and Archaeal cells use selenium structurally in selenouridine-modified tRNAs, in proteins translated with selenocysteine, and in the selenium-dependent molybdenum hydroxylases (SDMH). The first two uses both require the selenophosphate synthetase gene, selD. Examining over 500 complete prokaryotic genomes fi...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-3-4

    authors: Haft DH,Self WT

    更新日期:2008-02-20 00:00:00

  • Is pre-Darwinian evolution plausible?

    abstract:BACKGROUND:This essay highlights critical aspects of the plausibility of pre-Darwinian evolution. It is based on a critical review of some better-known open, far-from-equilibrium system-based scenarios supposed to explain processes that took place before Darwinian evolution had emerged and that resulted in the origin o...

    journal_title:Biology direct

    pub_type: 杂志文章,评审

    doi:10.1186/s13062-018-0216-7

    authors: Tessera M

    更新日期:2018-09-21 00:00:00

  • Optimal treatment and stochastic modeling of heterogeneous tumors.

    abstract:UNLABELLED:In this work we review past articles that have mathematically studied cancer heterogeneity and the impact of this heterogeneity on the structure of optimal therapy. We look at past works on modeling how heterogeneous tumors respond to radiotherapy, and take a particularly close look at how the optimal radiot...

    journal_title:Biology direct

    pub_type: 杂志文章,评审

    doi:10.1186/s13062-016-0142-5

    authors: Badri H,Leder K

    更新日期:2016-08-23 00:00:00

  • xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation.

    abstract:BACKGROUND:While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-016-0163-0

    authors: Yap CK,Eisenhaber B,Eisenhaber F,Wong WC

    更新日期:2016-11-29 00:00:00

  • Trees and networks before and after Darwin.

    abstract::It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context. By the mid-Eighteenth century the Great Chain of Being was increasingly seen to be an inadequate descript...

    journal_title:Biology direct

    pub_type: 历史文章,杂志文章,评审

    doi:10.1186/1745-6150-4-43

    authors: Ragan MA

    更新日期:2009-11-16 00:00:00

  • Episodic, transient systemic acidosis delays evolution of the malignant phenotype: Possible mechanism for cancer prevention by increased physical activity.

    abstract:BACKGROUND:The transition from premalignant to invasive tumour growth is a prolonged multistep process governed by phenotypic adaptation to changing microenvironmental selection pressures. Cancer prevention strategies are required to interrupt or delay somatic evolution of the malignant invasive phenotype. Empirical st...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-5-22

    authors: Smallbone K,Maini PK,Gatenby RA

    更新日期:2010-04-20 00:00:00

  • Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.

    abstract:BACKGROUND:In eukaryotes, RNA interference (RNAi) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mRNAs. The RNAi systems recognize the target RNA molecules via small guide RNAs that are completely or partially complementary to a region of the ta...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-4-29

    authors: Makarova KS,Wolf YI,van der Oost J,Koonin EV

    更新日期:2009-08-25 00:00:00

  • LINEs of evidence: noncanonical DNA replication as an epigenetic determinant.

    abstract::LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They are capable of synthesizing DNA on their own RNA templates by harnessing reverse transcriptase (RT) that they encode. Abundantly expressed full-length L1s and their RT are found to globally influence gene expression profiles, differentiati...

    journal_title:Biology direct

    pub_type: 杂志文章,评审

    doi:10.1186/1745-6150-8-22

    authors: Belan E

    更新日期:2013-09-13 00:00:00

  • Pathophysiology of Crohn's disease inflammation and recurrence.

    abstract::Chron's Disease is a chronic inflammatory intestinal disease, first described at the beginning of the last century. The disease is characterized by the alternation of periods of flares and remissions influenced by a complex pathogenesis in which inflammation plays a key role. Crohn's disease evolution is mediated by a...

    journal_title:Biology direct

    pub_type: 杂志文章,评审

    doi:10.1186/s13062-020-00280-5

    authors: Petagna L,Antonelli A,Ganini C,Bellato V,Campanelli M,Divizia A,Efrati C,Franceschilli M,Guida AM,Ingallinella S,Montagnese F,Sensi B,Siragusa L,Sica GS

    更新日期:2020-11-07 00:00:00

  • Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

    abstract:BACKGROUND:H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homolo...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-9-5

    authors: Zhou H,Gao S,Nguyen NN,Fan M,Jin J,Liu B,Zhao L,Xiong G,Tan M,Li S,Wong L

    更新日期:2014-04-08 00:00:00

  • A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands.

    abstract:BACKGROUND:Domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. RESULTS:Using sensitive sequence and structure similarity searches we identify a novel superfamily containing the bet...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-2-4

    authors: Burroughs AM,Balaji S,Iyer LM,Aravind L

    更新日期:2007-01-24 00:00:00

  • Activating and inhibiting connections in biological network dynamics.

    abstract:BACKGROUND:Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior--for e...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-3-49

    authors: McDonald D,Waterbury L,Knight R,Betterton MD

    更新日期:2008-12-04 00:00:00

  • MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases.

    abstract::The provenance and biochemical roles of eukaryotic MORC proteins have remained poorly understood since the discovery of their prototype MORC1, which is required for meiotic nuclear division in animals. The MORC family contains a combination of a gyrase, histidine kinase, and MutL (GHKL) and S5 domains that together co...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-3-8

    authors: Iyer LM,Abhiman S,Aravind L

    更新日期:2008-03-17 00:00:00