Molecular Systematics: Access to Nucleotide Sequence Information

2011 ◽  
pp. 42-42 ◽  
Keyword(s):  
Nucleotide Sequence ◽  
Molecular Systematics ◽  
Sequence Information ◽  
Nucleotide Sequence Information

Revision of Australian jumping spider genus Servaea Simon 1887 (Aranaea: Salticidae) including use of DNA sequence data and predicted distributions

Zootaxa ◽  
2012 ◽  
Vol 3350 (1) ◽  
pp. 1 ◽  
Author(s):  
BARRY J. RICHARDSON ◽  
NICOLE L. GUNTER
Keyword(s):  
Nucleotide Sequence ◽  
Dna Sequence ◽  
Type Species ◽  
Sequence Data ◽  
Sandy Soils ◽  
Soil Types ◽  
Sequence Information ◽  
Suitable Material ◽  
Dna Sequence Data ◽  
Nucleotide Sequence Information

The genus Servaea Simon 1887 is revised and redefined. Descriptions and identification keys are provided to the following sixspecies, of which three are described as new: Servaea incana (Karsch 1878), Servaea narraweena n. sp., Servaea melaina n.sp., Servaea spinibarbis Simon 1909, Servaea villosa (Keyserling 1881) and Servaea zabkai n. sp. The type species of thegenus, Servaea vestita (L. Koch 1879), is proposed here to be a junior synonym of Servaea incana. In addition to the diagnosesand descriptions, distributional and nucleotide sequence information are provided. DNA sequence data for the segment of COIused in other salticid studies was obtained for the five species for which suitable material was available. Intraspecific variationin S. villosa and S. incana were studied in more detail. Within-species divergence was S. melaina and S spinibarbis, had adjacent predicted distributions, one coastal on sandy soils and one inland on other soil types.

scholarly journals Revealing the Presence of a Symbolic Sequence Representing Multiple Nucleotides Based on K-Means Clustering of Oligonucleotides

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 348
Author(s):  
Byoungsang Lee ◽  
So Yeon Ahn ◽  
Charles Park ◽  
James J. Moon ◽  
Jung Heon Lee ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Clustering Algorithm ◽  
Sequence Information ◽  
Symbolic Sequence ◽  
Representative Sequence ◽  
Combined Application ◽  
The Social ◽  
The Common ◽  
Hybridization Profile ◽  
Common Sequence

In biological systems, a few sequence differences diversify the hybridization profile of nucleotides and enable the quantitative control of cellular metabolism in a cooperative manner. In this respect, the information required for a better understanding may not be in each nucleotide sequence, but representative information contained among them. Existing methodologies for nucleotide sequence design have been optimized to track the function of the genetic molecule and predict interaction with others. However, there has been no attempt to extract new sequence information to represent their inheritance function. Here, we tried to conceptually reveal the presence of a representative sequence from groups of nucleotides. The combined application of the K-means clustering algorithm and the social network analysis theorem enabled the effective calculation of the representative sequence. First, a “common sequence” is made that has the highest hybridization property to analog sequences. Next, the sequence complementary to the common sequence is designated as a ‘representative sequence’. Based on this, we obtained a representative sequence from multiple analog sequences that are 8–10-bases long. Their hybridization was empirically tested, which confirmed that the common sequence had the highest hybridization tendency, and the representative sequence better alignment with the analogs compared to a mere complementary.

scholarly journals Characterization of genomic PIG-A gene: a gene for glycosylphosphatidylinositol-anchor biosynthesis and paroxysmal nocturnal hemoglobinuria

Blood ◽  
1994 ◽  
Vol 83 (11) ◽  
pp. 3126-3131
Author(s):  
Y Iida ◽  
J Takeda ◽  
T Miyata ◽  
N Inoue ◽  
J Nishimura ◽  
...  
Keyword(s):  
Blood Cells ◽  
Paroxysmal Nocturnal Hemoglobinuria ◽  
Somatic Mutations ◽  
Surface Expression ◽  
Sequence Information ◽  
Chain Reaction ◽  
Nucleotide Sequence Information ◽  
Flanking Region ◽  
Polymerase Chain

Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired hemolytic anemia characterized by the presence of abnormal subpopulations of blood cells that are deficient in surface expression of glycosylphosphatidylinositol (GPI)-anchored proteins. Recent studies showed that the gene termed PIG-A, which participates in the first step of GPI-anchor biosynthesis, is mutated in the abnormal blood cells from patients with PNH. In this study the genomic PIG-A gene was cloned and characterized to obtain nucleotide sequence information for analyzing somatic mutations of PIG-A in patients with PNH. The PIG-A gene is at least 17 kb long and has six exons. The exon-intron boundaries and 583 bp of the 5′ flanking region were sequenced. The 5′ flanking region has no TATA-like sequence, but includes four CAAT boxes, two AP-2 sequences, and a CRE sequence, some of which are present in regions necessary for the promoter activity. We report pairs of oligonucleotide primers for polymerase chain reaction that should be useful to amplify and analyze various regions of the PIG-A gene in patients with PNH.

scholarly journals The mouse collagen X gene: complete nucleotide sequence, exon structure and expression pattern

1993 ◽  
Vol 289 (1) ◽  
pp. 247-253 ◽  
Author(s):  
K Elima ◽  
I Eerola ◽  
R Rosati ◽  
M Metsäranta ◽  
S Garofalo ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Transcription Start Site ◽  
Nucleotide Sequencing ◽  
Sequence Information ◽  
Collagen Gene ◽  
Start Site ◽  
Coding Region ◽  
Transcription Start ◽  
X Gene ◽  
Exon Structure

Overlapping genomic clones covering the 7.2 kb mouse alpha 1(X) collagen gene, 0.86 kb of promoter and 1.25 kb of 3′-flanking sequences were isolated from two genomic libraries and characterized by nucleotide sequencing. Typical features of the gene include a unique three-exon structure, similar to that in the chick gene, with the entire triple-helical domain of 463 amino acids coded by a single large exon. The highest degree of amino acid and nucleotide sequence conservation was seen in the coding region for the collagenous and C-terminal non-collagenous domains between the mouse and known chick, bovine and human collagen type X sequences. More divergence between the sequences occurred in the N-terminal non-collagenous domain. Similarity between the mammalian collagen X sequences extended into the 3′-untranslated sequence, particularly near the polyadenylation site. The promoter of the mouse collagen X gene was found to contain two TATAA boxes 159 bp apart; primer extension analyses of the transcription start site revealed that both were functional. The promoter has an unusual structure with a very low G + C content of 28% between positions -220 and -1 of the upstream transcription start site. Northern and in situ hybridization analyses confirmed that the expression of the alpha 1(X) collagen gene is restricted to hypertrophic chondrocytes in tissues undergoing endochondral calcification. The detailed sequence information of the gene is useful for studies on the promoter activity of the gene and for generation of transgenic mice.

scholarly journals Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature

2021 ◽  
Author(s):  
Matthias Lange ◽  
Blaise Alako ◽  
Guy Cochrane ◽  
Mehmood Ghaffar ◽  
Martin Mascher ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Web Application ◽  
Biological Diversity ◽  
Sequence Data ◽  
Geographical Information ◽  
Convention On Biological Diversity ◽  
Sequence Information ◽  
Nucleotide Sequence Data ◽  
Provenance Information ◽  
Quality Review

Background: Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSDs provenance, scientific use, and re-use in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level. Findings: For this data note, we extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. Flat data tables and an data warehouse with an interactive web application were constructed to enable ad hoc exploration of NSD use and summary statistics. Conclusions: The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enables scientists around the world to join literature and sequence databases in a multidimensional fashion. As a concrete use case, statistics of country clusters were visualized with respect to NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.

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