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... Jalan Kamper, Kampus IPB, Darmaga Bogor 16680. Indonesia Cucumber mosaic virus strain soybean (CMV-S) is one of economically important virus infecting soybean in Indonesia. However, it is very few information related with the CMV-S Indonesia isolates. Thus, the aim of present work is to detect and i ...
... Jalan Kamper, Kampus IPB, Darmaga Bogor 16680. Indonesia Cucumber mosaic virus strain soybean (CMV-S) is one of economically important virus infecting soybean in Indonesia. However, it is very few information related with the CMV-S Indonesia isolates. Thus, the aim of present work is to detect and i ...
BioPerf: A Benchmark Suite to Evaluate High-Performance
... Bioinformatics is a field for which the problems themselves are not thoroughly categorized, and many of the computational problems are NP-hard. This has led to the development of heuristics to solve the problems, giving sub-optimal results within a reasonable degree of accuracy quickly. Thus, the fi ...
... Bioinformatics is a field for which the problems themselves are not thoroughly categorized, and many of the computational problems are NP-hard. This has led to the development of heuristics to solve the problems, giving sub-optimal results within a reasonable degree of accuracy quickly. Thus, the fi ...
Nucleotide sequence diversity at the alcohol
... DNA sequence diversity has been studied in a very small number of plant species to date. These studies have concentrated on the agronomic crops maize [Zea mays (13, 14)] and pearl millet [Pennisetum glaucum (15)]. Studies of Adh sequence diversity have also been published for Arabidopsis thaliana (1 ...
... DNA sequence diversity has been studied in a very small number of plant species to date. These studies have concentrated on the agronomic crops maize [Zea mays (13, 14)] and pearl millet [Pennisetum glaucum (15)]. Studies of Adh sequence diversity have also been published for Arabidopsis thaliana (1 ...
Genomic organization of lignin peroxidase genes of Phanerochaete
... polymorphisms may also be related to variations in LiP activity. In P. falicurum, polymorphisms are caused by homologous recombination in distal regions of chromosomes, and it has been suggested that recombination in these dynamic regions might be related to antigenic variation (28). Extensive mappi ...
... polymorphisms may also be related to variations in LiP activity. In P. falicurum, polymorphisms are caused by homologous recombination in distal regions of chromosomes, and it has been suggested that recombination in these dynamic regions might be related to antigenic variation (28). Extensive mappi ...
IDO-Staph-Goldfain
... referred to as the integration site sequence for SCC (ISS), which serves as a target for ccr-mediated recombination, and • (4) the presence of flanking direct repeat sequences containing the ...
... referred to as the integration site sequence for SCC (ISS), which serves as a target for ccr-mediated recombination, and • (4) the presence of flanking direct repeat sequences containing the ...
Nomenclature for incompletely specified bases in nucleic acid
... the RNA. Similarly, no distinction will be made in the symbols between base, nucleoside and nucleotide. Sequences may be assumed to have a deoxyribose backbone (DNA) unless specified otherwise. These changes from earlier recommendations [1] reflect great advances in techniques for sequencing DNA, so ...
... the RNA. Similarly, no distinction will be made in the symbols between base, nucleoside and nucleotide. Sequences may be assumed to have a deoxyribose backbone (DNA) unless specified otherwise. These changes from earlier recommendations [1] reflect great advances in techniques for sequencing DNA, so ...
For the last three and a half billion years, evolution has been
... Hva er bioinformatikk? The NIH Biomedical Information Science and Technology Initiative Consortium agreed on the following definitions of bioinformatics and computational biology recognizing that no ...
... Hva er bioinformatikk? The NIH Biomedical Information Science and Technology Initiative Consortium agreed on the following definitions of bioinformatics and computational biology recognizing that no ...
Pyruvate-Phosphate Dikinase of Oxymonads and
... Phylogeny and evolution of PPDK. Although they share many metabolic similarities, eukaryotic microbes with PPilinked glycolysis are not all closely related to one another (26). This was noted some time ago (25, 26), and it was debated whether their metabolism was retained from an ancient ancestor or ...
... Phylogeny and evolution of PPDK. Although they share many metabolic similarities, eukaryotic microbes with PPilinked glycolysis are not all closely related to one another (26). This was noted some time ago (25, 26), and it was debated whether their metabolism was retained from an ancient ancestor or ...
Exons and Introns Characterization in Nucleic Acid Sequences by
... proteins to form the "spliceosome" complex that is responsible of recognizing the sites where the intron starts and ends, cutting them, expelling them from the pre-mRNA transcript and then assembling the exons to form mRNA [3]. For each intron, four nucleotide sequences work as signals that report t ...
... proteins to form the "spliceosome" complex that is responsible of recognizing the sites where the intron starts and ends, cutting them, expelling them from the pre-mRNA transcript and then assembling the exons to form mRNA [3]. For each intron, four nucleotide sequences work as signals that report t ...
Guide Tree
... Gap penalties for closely related sequences are lowered compared to more distantly related sequences. It is thought that those gaps occur in regions that do not disrupt the structure or function. Gap penalties increase when required at 8 residues or less for alignment. Because the minimum functional ...
... Gap penalties for closely related sequences are lowered compared to more distantly related sequences. It is thought that those gaps occur in regions that do not disrupt the structure or function. Gap penalties increase when required at 8 residues or less for alignment. Because the minimum functional ...
NSPCD LABORATORIES - World Health Organization
... Restrict analysis to discrete set of isolates (≤30) Identify “index isolate” as starting point for analysis that is defined on the basis of: • Epidemiological data (first case in an outbreak) • Clinical data (initial isolate from patient with multiple infections) • Strain typing data (most common st ...
... Restrict analysis to discrete set of isolates (≤30) Identify “index isolate” as starting point for analysis that is defined on the basis of: • Epidemiological data (first case in an outbreak) • Clinical data (initial isolate from patient with multiple infections) • Strain typing data (most common st ...
Automatic identification of topic boundaries in
... complementary algorithms for analysis. Interactive modules that provide the user with options for data sources and software tools, also allows the user to customize the rendering and visualization of the outputs. An additional feature allows the registered user to maintain a personalized page contai ...
... complementary algorithms for analysis. Interactive modules that provide the user with options for data sources and software tools, also allows the user to customize the rendering and visualization of the outputs. An additional feature allows the registered user to maintain a personalized page contai ...
Dynamic Programming: Sequence alignment
... Rapid approximation of MSP score • BLAST minimizes time spent on database sequences whose similarity with the query has little chance of exceeding this cutoff S. • Main strategy: seek only segment pairs (one from database, one query) that contain a word pair with score >= T • Intuition: If the sequ ...
... Rapid approximation of MSP score • BLAST minimizes time spent on database sequences whose similarity with the query has little chance of exceeding this cutoff S. • Main strategy: seek only segment pairs (one from database, one query) that contain a word pair with score >= T • Intuition: If the sequ ...
BLAST: Basic Local Alignment Search Tool Altschul et al. J. Mol Bio
... Rapid approximation of MSP score • BLAST minimizes time spent on database sequences whose similarity with the query has little chance of exceeding this cutoff S. • Main strategy: seek only segment pairs (one from database, one query) that contain a word pair with score >= T • Intuition: If the sequ ...
... Rapid approximation of MSP score • BLAST minimizes time spent on database sequences whose similarity with the query has little chance of exceeding this cutoff S. • Main strategy: seek only segment pairs (one from database, one query) that contain a word pair with score >= T • Intuition: If the sequ ...
Supplementary Information to manuscript Microbial life in the Lake
... See Text S5 for details on phylogenetic analyses. Neighbor-joining analysis using 1000 bootstrap replicates was used to infer tree topology. The scale bar represents 10% of sequence divergence. Bootstrap values are indicated at branch points as open (>50%) and closed (>75%) circles. Sequences obtain ...
... See Text S5 for details on phylogenetic analyses. Neighbor-joining analysis using 1000 bootstrap replicates was used to infer tree topology. The scale bar represents 10% of sequence divergence. Bootstrap values are indicated at branch points as open (>50%) and closed (>75%) circles. Sequences obtain ...
Molecular characterization of two Bangladeshi infectious bursal
... second ORF encodes a 110-kDa polyprotein, which is autocatalytically cleaved [12,26] to produce viral proteins VP2 (40 kDa), VP4 (28 kDa), and VP3 (32 kDa). Using sequence analysis and reverse genetics, VP2 from segment A [34,36], VP1 from segment B [14], or both [2,3] have been found to contribute ...
... second ORF encodes a 110-kDa polyprotein, which is autocatalytically cleaved [12,26] to produce viral proteins VP2 (40 kDa), VP4 (28 kDa), and VP3 (32 kDa). Using sequence analysis and reverse genetics, VP2 from segment A [34,36], VP1 from segment B [14], or both [2,3] have been found to contribute ...
What is sequence alignment - department of computer & electrical
... sequence, perhaps introducing gaps, such that the total score is optimal. “Optimal” alignment Alignment with best score relative to metrics used May or may not have biological significance ...
... sequence, perhaps introducing gaps, such that the total score is optimal. “Optimal” alignment Alignment with best score relative to metrics used May or may not have biological significance ...
The sequence of the tms transcript 2 locus of the A. tumefaciens
... In E_;_ coli the consensus promoter sequence is composed of a -10 sequence, TATAAT, and a -35 sequence, TTGACA (the positions are relative to transcription start)(35-36). The transcript 2 gene has a "TATA" like sequence as pointed out above; it does not, however, have a -35 sequence. Another importa ...
... In E_;_ coli the consensus promoter sequence is composed of a -10 sequence, TATAAT, and a -35 sequence, TTGACA (the positions are relative to transcription start)(35-36). The transcript 2 gene has a "TATA" like sequence as pointed out above; it does not, however, have a -35 sequence. Another importa ...
- Biological Sciences
... incomplete and are presumably completed posttranscriptionally by polyadenylation. The stop codons TAG and AGG seem to be used twice and once, respectively, whereas the stop codon AGA is not used. The start codon ATG is utilized in seven genes, and ATT is used four and ATA two times. The genes are or ...
... incomplete and are presumably completed posttranscriptionally by polyadenylation. The stop codons TAG and AGG seem to be used twice and once, respectively, whereas the stop codon AGA is not used. The start codon ATG is utilized in seven genes, and ATT is used four and ATA two times. The genes are or ...
Document
... kinase domain can make weak but relevant matches to other domain types appear very low in the hit list, so that they are missed (e.g. only appearing after 5000 kinase hits) • Sequences containing low-complexity regions, such as coiled coils and transmembrane regions, can cause an explosion of the se ...
... kinase domain can make weak but relevant matches to other domain types appear very low in the hit list, so that they are missed (e.g. only appearing after 5000 kinase hits) • Sequences containing low-complexity regions, such as coiled coils and transmembrane regions, can cause an explosion of the se ...
discovery of new enzymes in extreme environments through
... Extremozymes expand the limits of biocatalysis – The information acquired from the study of extremozymes makes it possible to modify enzymes to improve their ranges of stability and activity (for industrial and medical applications) However, the organisms living in extreme environments are hard to b ...
... Extremozymes expand the limits of biocatalysis – The information acquired from the study of extremozymes makes it possible to modify enzymes to improve their ranges of stability and activity (for industrial and medical applications) However, the organisms living in extreme environments are hard to b ...
ICBEnzyEvol
... combination of codons. But generation of all sequences is infeasible because of very large time and space complexity. We use here this reverse mechanism, to match the closely related nucleotide sequences of the respective amino acids. The next slide will show, what method we have used to proceed wit ...
... combination of codons. But generation of all sequences is infeasible because of very large time and space complexity. We use here this reverse mechanism, to match the closely related nucleotide sequences of the respective amino acids. The next slide will show, what method we have used to proceed wit ...
Metz and Palumbi 1996
... amino acid sequences of mature Echinometru bindin showing species-specific and polymorphic variation. Alignment is based on nucleotide sequences, including information at silent sites. Labels denote species (M: Echinometru mathaei; 0: E. oblongu; A: Echinometru species type ‘A’) obtained from Hawaii ...
... amino acid sequences of mature Echinometru bindin showing species-specific and polymorphic variation. Alignment is based on nucleotide sequences, including information at silent sites. Labels denote species (M: Echinometru mathaei; 0: E. oblongu; A: Echinometru species type ‘A’) obtained from Hawaii ...
Nucleic Acids Research
... on a standard typewriter keyboard; (v) historical precedence. 3.1 Guanine, adenine, thymine, cytosine: G, A, T, C These one-letter symbols have previously been established [1] and are generally used. There is, however, a problem of discriminating between the upper case letters G and C on poorly copi ...
... on a standard typewriter keyboard; (v) historical precedence. 3.1 Guanine, adenine, thymine, cytosine: G, A, T, C These one-letter symbols have previously been established [1] and are generally used. There is, however, a problem of discriminating between the upper case letters G and C on poorly copi ...
Sequences of the Nucleocapsid Genes from Two Strains of Avian
... enriched in basic residues with an overall positive charge at neutral p H of 19 for Beaudette and 20 for M41. These basic residues are clustered in distinct regions; for example, in the Beaudette sequence the regions from bases 727 to 791 and from 1167 to 1205. The C-terminus of the polypeptide is, ...
... enriched in basic residues with an overall positive charge at neutral p H of 19 for Beaudette and 20 for M41. These basic residues are clustered in distinct regions; for example, in the Beaudette sequence the regions from bases 727 to 791 and from 1167 to 1205. The C-terminus of the polypeptide is, ...