PARALLEL SYNTENIC ALIGNMENTS

Given two genomic DNA sequences, the syntenic alignment problem is to compute an ordered list of subsequences for each sequence such that the corresponding subsequence pairs exhibit a high degree of similarity. Syntenic alignments are useful in comparing genomic DNA from related species and in identifying conserved genes. In this paper, we present a parallel algorithm for computing syntenic alignments that runs in [Formula: see text] time, where m and n are the respective lengths of the two genomic sequences, and p is the number of processors used. Our algorithm is time optimal with respect to the corresponding sequential algorithm and can use [Formula: see text] processors, where n is the length of the larger sequence. The space requirement of the algorithm is [Formula: see text] per processor. Using an implementation of this parallel algorithm, we report the alignment of a gene-rich region of human chromosome 12, namely 12p13 and its syntenic region in mouse chromosome 6 (both over 220,000 base pairs in length) in under 24 minutes on a 64-processor IBM xSeries cluster.

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Analysis and Characterization of the Complete Genome of Tupaia (Tree Shrew) Herpesvirus

Journal of Virology ◽

10.1128/jvi.75.10.4854-4870.2001 ◽

2001 ◽

Vol 75 (10) ◽

pp. 4854-4870 ◽

Cited By ~ 33

Author(s):

Udo Bahr ◽

Gholamreza Darai

Keyword(s):

Dna Sequences ◽

Tree Shrew ◽

Biological Properties ◽

Open Reading Frames ◽

Murine Cytomegalovirus ◽

Unique Region ◽

Viral Genes ◽

Conserved Genes ◽

Dna Strands ◽

High Degree

ABSTRACT The tupaia herpesvirus (THV) was isolated from spontaneously degenerating tissue cultures of malignant lymphoma, lung, and spleen cell cultures of tree shrews (Tupaia spp.). The determination of the complete nucleotide sequence of the THV strain 2 genome resulted in a 195,857-bp-long, linear DNA molecule with a G+C content of 66.5%. The terminal regions of the THV genome and the loci of conserved viral genes were found to be G+C richer. Furthermore, no large repetitive DNA sequences could be identified. This is in agreement with the previous classification of THV as the prototype species of herpesvirus genome group F. The search for potential coding regions resulted in the identification of 158 open reading frames (ORFs) regularly distributed on both DNA strands. Seventy-six out of the 158 ORFs code for proteins that are significantly homologous to known herpesvirus proteins. The highest homologies found were to primate and rodent cytomegaloviruses. Biological properties, protein homologies, the arrangement of conserved viral genes, and phylogenetic analysis revealed that THV is a member of the subfamilyBetaherpesvirinae. The evolutionary lineages of THV and the cytomegaloviruses seem to have branched off from a common ancestor. In addition, it was found that the arrangements of conserved genes of THV and murine cytomegalovirus strain Smith, both of which are not able to form genomic isomers, are colinear with two different human cytomegalovirus (HCMV) strain AD169 genomic isomers that differ from each other in the orientation of the long unique region. The biological properties and the high degree of relatedness of THV to the mammalian cytomegaloviruses allow the consideration of THV as a model system for investigation of HCMV pathogenicity.

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Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana

Genome ◽

10.1139/g99-033 ◽

1999 ◽

Vol 42 (5) ◽

pp. 887-892 ◽

Cited By ~ 15

Author(s):

Anne-Marie van Dodeweerd ◽

Caroline R Hall ◽

Elisabeth G Bent ◽

Samantha J Johnson ◽

Michael W Bevan ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Dna Sequences ◽

Genomic Dna ◽

Genome Structure ◽

Plant Genome ◽

Fine Scale ◽

Plant Genomics ◽

Homologous Genes ◽

Conserved Genes ◽

Plant Genome Evolution

Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved framework of genes identified is interspersed with non-conserved genes, indicating that mechanisms beyond segmental inversions and translocations need to be invoked to fully explain plant genome evolution, and that the benefits of comparative genomics over such large taxonomic distances may be limited.Key words: plant genomics, comparative mapping.

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EFFICIENT ALGORITHMS FOR THE EUCLIDEAN DISTANCE TRANSFORM

Parallel Processing Letters ◽

10.1142/s0129626495000187 ◽

1995 ◽

Vol 05 (02) ◽

pp. 205-212 ◽

Cited By ~ 16

Author(s):

SANDY PAVEL ◽

SELIM G. AKL

Keyword(s):

Parallel Algorithm ◽

Euclidean Distance ◽

Sequential Algorithm ◽

Distance Transform ◽

Binary Images ◽

Euclidean Distance Transform ◽

Erew Pram ◽

Time Optimal ◽

Time Bounds ◽

And Robotics

The Euclidean Distance Transform is an important computational tool for the processing of binary images, with applications in many areas such as computer vision, pattern recognition and robotics. We investigate the properties of this transform and describe an O(n2) time optimal sequential algorithm. A deterministic EREW-PRAM parallel algorithm which runs in O( log n) time using O(n2) processors and O(n2) space is also derived. Further, a cost optimal randomized parallel algorithm which runs within the same time bounds with high probability, is given.

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Evidence for genetic diversity in Trypanosoma (Nannomonas) congolense

Parasitology ◽

10.1017/s0031182000051465 ◽

1986 ◽

Vol 93 (2) ◽

pp. 291-304 ◽

Cited By ~ 32

Author(s):

P. A. O. Majiva ◽

R. Hamers ◽

N. Van Meirvenne ◽

G. Matthyssens

Keyword(s):

Genetic Diversity ◽

Trypanosoma Brucei ◽

Restriction Enzyme ◽

Dna Sequences ◽

Genomic Dna ◽

Trypanosoma Congolense ◽

Synthetic Oligonucleotide ◽

Hybridization Probes ◽

Conserved Genes ◽

Variant Antigen

SUMMARYGenetic proximity between two karyotypic groups of Trypanosoma congolense was investigated using as hybridization probes: (i) total genomic DNA, (ii) a 35 nucleotide long synthetic oligonucleotide, and (iii) non-variant antigen type (non-VAT) specific complementary DNAs. The phylogenetic relationship between Trypanosoma brucei and T. evansi, both of which are accepted species in the subgenus Trypanozoon, was used as a reference to assess the phylogenetic proximity of the two groups of T. congolense. Results indicate that some morphologically indistinguishable T. congolense populations differ in a variety of molecular and genetic properties: molecular karyotypes, majority of the DNA sequences, and the restriction enzyme sites in the genomic environments of various conserved genes. The implications of these findings for trypanosome evolution and T. congolense epidemiology are discussed.

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DETERMINING THE SEPARATION OF SIMPLE POLYGONS

International Journal of Computational Geometry & Applications ◽

10.1142/s0218195994000240 ◽

1994 ◽

Vol 04 (04) ◽

pp. 457-474 ◽

Cited By ~ 7

Author(s):

NANCY M. AMATO

Keyword(s):

Parallel Algorithm ◽

Time Complexity ◽

Minimum Distance ◽

Sequential Algorithm ◽

Parallel Methods ◽

Simple Polygons ◽

Closest Pair ◽

Time Optimal ◽

Crew Pram

Given simple polygons P and Q, their separation, denoted by σ(P, Q), is defined to be the minimum distance between their boundaries. We present a parallel algorithm for finding a closest pair among all pairs (p, q), p ∈ P and q ∈ Q. The algorithm runs in O ( log n) time using O(n) processors on a CREW PRAM, where n = |P| + |Q|. This algorithm is time-optimal and improves by a factor of O ( log n) on the time complexity of previous parallel methods. The algorithm can be implemented serially in Θ (n) time, which gives the first optimal sequential algorithm for determining the separation of simple polygons. Our results are obtained by providing a unified treatment of the separation and the closest visible vertex problems for simple polygons.

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Developing a Genetic System in Deinococcus radiodurans for Analyzing Mutations

Genetics ◽

10.1093/genetics/166.2.661 ◽

2004 ◽

Vol 166 (2) ◽

pp. 661-668

Author(s):

Mandy Kim ◽

Erika Wolff ◽

Tiffany Huang ◽

Lilit Garibyan ◽

Ashlee M Earl ◽

...

Keyword(s):

Dna Sequences ◽

Deinococcus Radiodurans ◽

Genetic System ◽

Base Change ◽

Base Substitution ◽

Wild Type ◽

Base Pairs ◽

E Coli ◽

Radiation Induced ◽

Induced Mutagenesis

Abstract We have applied a genetic system for analyzing mutations in Escherichia coli to Deinococcus radiodurans, an extremeophile with an astonishingly high resistance to UV- and ionizing-radiation-induced mutagenesis. Taking advantage of the conservation of the β-subunit of RNA polymerase among most prokaryotes, we derived again in D. radiodurans the rpoB/Rif r system that we developed in E. coli to monitor base substitutions, defining 33 base change substitutions at 22 different base pairs. We sequenced >250 mutations leading to Rif r in D. radiodurans derived spontaneously in wild-type and uvrD (mismatch-repair-deficient) backgrounds and after treatment with N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and 5-azacytidine (5AZ). The specificities of NTG and 5AZ in D. radiodurans are the same as those found for E. coli and other organisms. There are prominent base substitution hotspots in rpoB in both D. radiodurans and E. coli. In several cases these are at different points in each organism, even though the DNA sequences surrounding the hotspots and their corresponding sites are very similar in both D. radiodurans and E. coli. In one case the hotspots occur at the same site in both organisms.

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Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

Beni-Suef University Journal of Basic and Applied Sciences ◽

10.1186/s43088-020-00094-4 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Kuldeepsingh A. Kalariya ◽

Ram Prasnna Meena ◽

Lipi Poojara ◽

Deepa Shahi ◽

Sandip Patel

Keyword(s):

Dna Sequences ◽

Genomic Dna ◽

Competitive Inhibition ◽

Sequence Data ◽

Homology Model ◽

Squalene Synthase ◽

Gymnema Sylvestre ◽

Gardenia Jasminoides ◽

Ramachandran Plots ◽

Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

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THE DNA OF CAENORHABDITIS ELEGANS

Genetics ◽

10.1093/genetics/77.1.95 ◽

1974 ◽

Vol 77 (1) ◽

pp. 95-104

Author(s):

J E Sulston ◽

S Brenner

Keyword(s):

Caenorhabditis Elegans ◽

Chemical Analysis ◽

Dna Sequences ◽

Base Composition ◽

Nematode Caenorhabditis Elegans ◽

5S Rna ◽

Base Pairs ◽

Small Component ◽

E Coli ◽

The Mean

ABSTRACT Chemical analysis and a study of renaturation kinetics show that the nematode, Caenorhabditis elegans, has a haploid DNA content of 8 x IO7 base pairs (20 times the genome of E. coli). Eighty-three percent of the DNA sequences are unique. The mean base composition is 36% GC; a small component, containing the rRNA cistrons, has a base composition of 51% GC. The haploid genome contains about 300 genes for 4s RNA, 110 for 5s RNA, and 55 for (18 + 28)S RNA.

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