Biomart/ GENOME ALIGNMENT III
... evolutionary history of species and in identifying functional regions in genomes. The possibilities for identifying regions under selection are enhanced with the addition of more sequences and this observation has led to numerous ‘focused sequencing’ projects which seek to obtain sequence for a smal ...
... evolutionary history of species and in identifying functional regions in genomes. The possibilities for identifying regions under selection are enhanced with the addition of more sequences and this observation has led to numerous ‘focused sequencing’ projects which seek to obtain sequence for a smal ...
MAK, a computational tool kit for automated MITE
... to belong to either type of element have been reported in plants and animals over the past decade (1–27). Because these families typically bear terminal inverted repeats (TIRs) and have target site duplications (TSDs) in their flanking sequences, they were given a collective name of miniature invert ...
... to belong to either type of element have been reported in plants and animals over the past decade (1–27). Because these families typically bear terminal inverted repeats (TIRs) and have target site duplications (TSDs) in their flanking sequences, they were given a collective name of miniature invert ...
A molecular method for assessing meiofauna diversity in marine
... found that using meiofauna data along with macrofauna data provides greater insight into the processes affecting a polluted area, since meiofauna are not as affected by physical disturbance as macrofauna. The cost of processing and identifying macrofauna is high and incorporating another component o ...
... found that using meiofauna data along with macrofauna data provides greater insight into the processes affecting a polluted area, since meiofauna are not as affected by physical disturbance as macrofauna. The cost of processing and identifying macrofauna is high and incorporating another component o ...
Origin and evolution of the slime molds (Mycetozoa)
... Mycetozoan tef Gene Sequences and Intron Positions. The 59 two-thirds of the Physarum tef gene was amplified from genomic DNA, while the 39 half of the gene was amplified from cDNA. The latter was necessary because all primer combinations for the 39 half of the gene preferentially amplified the retr ...
... Mycetozoan tef Gene Sequences and Intron Positions. The 59 two-thirds of the Physarum tef gene was amplified from genomic DNA, while the 39 half of the gene was amplified from cDNA. The latter was necessary because all primer combinations for the 39 half of the gene preferentially amplified the retr ...
A Plastid in the Making: Evidence for a Second
... new rDNA sequences were combined with database sequences to construct an alignment that contained the genes encoding SSU rRNA, tRNAIle, tRNA-Ala, and LSU rRNA. Most sequences came from completed or ongoing (‘shotgun’) genome projects, whereas in some cases, separate entries for SSU and LSU rRNA gene ...
... new rDNA sequences were combined with database sequences to construct an alignment that contained the genes encoding SSU rRNA, tRNAIle, tRNA-Ala, and LSU rRNA. Most sequences came from completed or ongoing (‘shotgun’) genome projects, whereas in some cases, separate entries for SSU and LSU rRNA gene ...
What`s new - JSI medical systems
... Min absolute coverage: This value refers to the absolute coverage at a position. Sequencepositions with a coverage below this value are written in grey (instead of black). Mutations/variations at those positons are not listed in the Variation/Mutation table. In case separated coverage is used and th ...
... Min absolute coverage: This value refers to the absolute coverage at a position. Sequencepositions with a coverage below this value are written in grey (instead of black). Mutations/variations at those positons are not listed in the Variation/Mutation table. In case separated coverage is used and th ...
Genetic Inversion: Relationships Among Species
... centromere. Any genes that were within this section of the chromosome have now been moved to a new position with the exception of the potential gene at the ‘pivot point.’ Illustrated a different way with numbers, let us start with the gene sequence 123456. If we invert the strip ‘234’ of the chromos ...
... centromere. Any genes that were within this section of the chromosome have now been moved to a new position with the exception of the potential gene at the ‘pivot point.’ Illustrated a different way with numbers, let us start with the gene sequence 123456. If we invert the strip ‘234’ of the chromos ...
UV-Targeted Dinucleotides Are Not Depleted in Light
... FIG. 2.—Plot of the mean zscore statistics for intergenic sequences (x axis) and for coding sequences (y axis), for each of the 4 pyrimidine dinucleotides. On each plot, a dot corresponds to the mean of these 2 statistics in a given prokaryote chromosome. The null x and y axis (dotted lines) and the ...
... FIG. 2.—Plot of the mean zscore statistics for intergenic sequences (x axis) and for coding sequences (y axis), for each of the 4 pyrimidine dinucleotides. On each plot, a dot corresponds to the mean of these 2 statistics in a given prokaryote chromosome. The null x and y axis (dotted lines) and the ...
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... not only because of the uncertain physiological role it plays in these organisms, which require oxygen to oxidize ammonia and generate energy (17), but also because it has been demonstrated that ammonia oxidizers, such as Nitrosomonas europaea, produce the environmentally important trace gases nitri ...
... not only because of the uncertain physiological role it plays in these organisms, which require oxygen to oxidize ammonia and generate energy (17), but also because it has been demonstrated that ammonia oxidizers, such as Nitrosomonas europaea, produce the environmentally important trace gases nitri ...
what is alignment? - UWI St. Augustine
... For comparing long DNA sequences with a short one Comparing a gene with a complete genome For detecting similarities between highly diverged sequences which still share common subsequences (that have little or no Jan 18, 2010 © UKK, Bioinformatics Centre, ...
... For comparing long DNA sequences with a short one Comparing a gene with a complete genome For detecting similarities between highly diverged sequences which still share common subsequences (that have little or no Jan 18, 2010 © UKK, Bioinformatics Centre, ...
Direct Sequence Analysis of the 14q+ and 18q
... requires the presence of the 5' recombination signals next to the junctional D, exon, lack of amplification may be due to removal of the 5' recombination signal sequence by a preceding V,-D, recombination. In addition, the D, primer includes part of the intervening sequence between the heptamer and ...
... requires the presence of the 5' recombination signals next to the junctional D, exon, lack of amplification may be due to removal of the 5' recombination signal sequence by a preceding V,-D, recombination. In addition, the D, primer includes part of the intervening sequence between the heptamer and ...
Mugisha, L., Leendertz, FH, Opuda-Asibo, J., Olobo, JO, Ehlers, B. A
... The members of the family Herpesviridae have been previously grouped into three subfamilies, designated Alphaherpesvirinae, Betaherpesvirinae and Gammaherpesvirinae [28], and phylogenetic lineages in these subfamilies were identified [22–25]. In studies amplifying unknown herpes virus sequences from ...
... The members of the family Herpesviridae have been previously grouped into three subfamilies, designated Alphaherpesvirinae, Betaherpesvirinae and Gammaherpesvirinae [28], and phylogenetic lineages in these subfamilies were identified [22–25]. In studies amplifying unknown herpes virus sequences from ...
Phylogenetic Relationships Among Ascomycetes: Evidence from an
... Mims, and Blackwell 1996). Euascomycetes are both the most complex in morphology and the most diverse group in the Ascomycota. The major characters used to delineate the principal lineages of Euascomycetes are the morphology of the fruiting body (ascocarp) and the structure of the ascus (Nannfeldt 1 ...
... Mims, and Blackwell 1996). Euascomycetes are both the most complex in morphology and the most diverse group in the Ascomycota. The major characters used to delineate the principal lineages of Euascomycetes are the morphology of the fruiting body (ascocarp) and the structure of the ascus (Nannfeldt 1 ...
File_details - Harvard PlasmID Database
... the target sequence or a nearby universal sequence (such as a cloning linker or the vector), this clone format is called “closed” (Examples C-E). Corollary: If your cloning strategy supplies a STOP codon in a 3’ universal sequence (such as a cloning linker or the vector) to the end of the coding seq ...
... the target sequence or a nearby universal sequence (such as a cloning linker or the vector), this clone format is called “closed” (Examples C-E). Corollary: If your cloning strategy supplies a STOP codon in a 3’ universal sequence (such as a cloning linker or the vector) to the end of the coding seq ...
LESSON 4 Understanding Genetic Tests to Detect BRCA1
... starting point. The workers don’t need to pay attention to the places where the beads align correctly—the colors are the same—just the places where the beads do not match the reference necklace. A BLAST alignment works in a similar way, although the actual method to align the sequences is not exactl ...
... starting point. The workers don’t need to pay attention to the places where the beads align correctly—the colors are the same—just the places where the beads do not match the reference necklace. A BLAST alignment works in a similar way, although the actual method to align the sequences is not exactl ...
Multifractal characterisation of length sequences of coding and
... One can study the DNA sequences in detail by considering the order in which four kinds of nucleotides of DNA are assembled, namely adenine (a), cytosine (c), guanine (g), and thymine (t). There has been considerable interest in the 3nding of long-range correlation (LRC) in DNA sequences at this leve ...
... One can study the DNA sequences in detail by considering the order in which four kinds of nucleotides of DNA are assembled, namely adenine (a), cytosine (c), guanine (g), and thymine (t). There has been considerable interest in the 3nding of long-range correlation (LRC) in DNA sequences at this leve ...
A method for fast database search for all k-nucleotide repeats
... tandem repeat. In the example above, we nd CTT repeated at an interval of 7 and conclude that CTTGCA could be a tandem repeat period. Note we are not looking speci cally for CTT , only for any 3 base string that repeats at an interval of 7. A pattern found by this method we denote a suspicious patt ...
... tandem repeat. In the example above, we nd CTT repeated at an interval of 7 and conclude that CTTGCA could be a tandem repeat period. Note we are not looking speci cally for CTT , only for any 3 base string that repeats at an interval of 7. A pattern found by this method we denote a suspicious patt ...
Consensus Clustering for Binning Metagenome Sequences
... In this paper we present a model based on consensus of different clustering models by the combination of different distances measures. The difference in the models are referred to the data use to train them. The data are reconstructed using different lengths of sequences. The proposed method is appl ...
... In this paper we present a model based on consensus of different clustering models by the combination of different distances measures. The difference in the models are referred to the data use to train them. The data are reconstructed using different lengths of sequences. The proposed method is appl ...
A large scale analysis of resistance gene
... P1B-fwd with P3D-rev, P1B-fwd with P3A-rev, P1A-fwd with P3D-rev, LM638 with P3A-rev, LM638 with P3D-rev, and LM638 with RNBS-D-rev. The positions of the primers are shown in Fig. 1. PCRs were performed in a 25-ll volume containing each dNTP at 200 lM, each primer at 1 lM, 1 U of Taq DNA polymerase, ...
... P1B-fwd with P3D-rev, P1B-fwd with P3A-rev, P1A-fwd with P3D-rev, LM638 with P3A-rev, LM638 with P3D-rev, and LM638 with RNBS-D-rev. The positions of the primers are shown in Fig. 1. PCRs were performed in a 25-ll volume containing each dNTP at 200 lM, each primer at 1 lM, 1 U of Taq DNA polymerase, ...
Evolution of Disintegrin Cysteine-Rich and
... stars). Some conserved positions among snake toxins are also shared with few, but not all, mammalian MDCs (Fig. 2, dots). Therefore, MDCs may be considered a family of proteins with high sequence similarity. However, the comparison of MDCs with MMPs reveals little sequence similarity (below 45%), th ...
... stars). Some conserved positions among snake toxins are also shared with few, but not all, mammalian MDCs (Fig. 2, dots). Therefore, MDCs may be considered a family of proteins with high sequence similarity. However, the comparison of MDCs with MMPs reveals little sequence similarity (below 45%), th ...
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... A Cartesian trajectory was used to fill the k-space with phase-encoding (y) in the anteroposterior direction. The field of view was covered by a 256 × 240 pixel matrix, and in-plane reconstruction was allowed to achieve an isotropic spatial resolution of 1.4 × 1.4 × 1.4 mm and a voxel size of 2.74 m ...
... A Cartesian trajectory was used to fill the k-space with phase-encoding (y) in the anteroposterior direction. The field of view was covered by a 256 × 240 pixel matrix, and in-plane reconstruction was allowed to achieve an isotropic spatial resolution of 1.4 × 1.4 × 1.4 mm and a voxel size of 2.74 m ...
Presence of a mitochondrial-type 70
... cDNA library. The insert was 1865 bp and showed an ORF of 609 amino acids. The codon usage is of the same pattern as for b-tubulin (26) and ferredoxin (27) genes of T. vaginalis. The 39-flanking region of the cDNA clone was A1T rich and short, as already noted (28, 29). The 59 end unfortunately was ...
... cDNA library. The insert was 1865 bp and showed an ORF of 609 amino acids. The codon usage is of the same pattern as for b-tubulin (26) and ferredoxin (27) genes of T. vaginalis. The 39-flanking region of the cDNA clone was A1T rich and short, as already noted (28, 29). The 59 end unfortunately was ...
Determination of the entire sequence of turtle CR1: the first open
... sequence of CR1 elements to characterize the entire structure of this family. Because these elements have 5’ truncations at various positions and, moreover, because only 2 kb of the sequence of chicken CR1 had been reported from the 3’ end, we adopted the strategy of gradual extension in the 5’ dire ...
... sequence of CR1 elements to characterize the entire structure of this family. Because these elements have 5’ truncations at various positions and, moreover, because only 2 kb of the sequence of chicken CR1 had been reported from the 3’ end, we adopted the strategy of gradual extension in the 5’ dire ...
Homologous and Nonhomologous Rearrangements: Interactions
... (positive when realizing a function, negative when inhibiting it). This means that the protein contributes to the range [m−w, m+w] of metabolic processes, with a preference for the processes closest to m (for which the highest efficiency, h, is reached). Thus, various types of proteins can co-exist, ...
... (positive when realizing a function, negative when inhibiting it). This means that the protein contributes to the range [m−w, m+w] of metabolic processes, with a preference for the processes closest to m (for which the highest efficiency, h, is reached). Thus, various types of proteins can co-exist, ...
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.Sequence alignments are also used for non-biological sequences, such as those present in natural language or in financial data.