Prediction of protein subeellular localization based on primary sequence data

2004 ◽  
Author(s):  
M. Ozarar ◽  
V. Atalay ◽  
R.C. Atalay
Keyword(s):  
Sequence Data ◽  
Primary Sequence ◽  
Primary Sequence Data

Molecular characterization of two insect nematode species (Oxyurida: Thelastomatidae) using small subunit (18S) ribosomal DNA sequence and secondary-structure analyses

2013 ◽  
Vol 88 (2) ◽  
pp. 219-229
Author(s):  
A. Chaudhary ◽  
N. Singh ◽  
H.S. Singh
Keyword(s):  
Secondary Structure ◽  
Molecular Characterization ◽  
Ribosomal Dna ◽  
Periplaneta Americana ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nematode Species ◽  
Small Subunit ◽  
Primary Sequence ◽  
Primary Sequence Data

AbstractNematodes of the family Thelastomatidae are parasitic in the alimentary tract of many arthropods, including Periplaneta americana L. In Meerut, Uttar Pradesh, India, two nematode species, namely Hammerschmidtiella indicus and Thelastoma icemi, belonging to this family have been reported. In the present study, the molecular phylogeny of these two nematode species was derived using small subunit (18S) sequence and secondary-structure analyses. The small subunit sequence analyses were carried out to explore the validation and systematics of these species. Phylogenetic analyses were performed for primary sequence data as well as using neighbour-joining and maximum-parsimony approaches. In contrast, the inferred secondary structures for the two species, using free-energy modelling, showed structural identities. As well as this, motif sequences were also found to be a promising tool for nematode species identification. The study provides molecular characterization based on primary sequence data of the 18S ribosomal DNA region of the nematodes along with secondary-structure data and motif sequences for inferences at higher taxonomic levels.

scholarly journals Amino acid distributions around O-linked glycosylation sites

1991 ◽  
Vol 275 (2) ◽  
pp. 529-534 ◽  
Author(s):  
I B Wilson ◽  
Y Gavel ◽  
G von Heijne
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Sequence Data ◽  
Prominent Feature ◽  
Primary Sequence ◽  
Hydroxy Amino ◽  
Glycosylation Sites ◽  
Sequence Requirements ◽  
Primary Sequence Data ◽  
Glycosylated Proteins

To study the sequence requirements for addition of O-linked N-acetylgalactosamine to proteins, amino acid distributions around 174 O-glycosylation sites were compared with distributions around non-glycosylated sites. In comparison with non-glycosylated serine and threonine residues, the most prominent feature in the vicinity of O-glycosylated sites is a significantly increased frequency of proline residues, especially at positions -1 and +3 relative to the glycosylated residues. Alanine, serine and threonine are also significantly increased. The high serine and threonine content of O-glycosylated regions is due to the presence of clusters of several closely spaced glycosylated hydroxy amino acids in many O-glycosylated proteins. Such clusters can be predicted from the primary sequence in some cases, but there is no apparent possibility of predicting isolated O-glycosylation sites from primary sequence data.

scholarly journals The biological improbability of a clone

2002 ◽  
Vol 79 (1) ◽  
pp. 1-9 ◽  
Author(s):  
GUGS LUSHAI ◽  
HUGH D. LOXDALE
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Genome Mapping ◽  
Sequence Data ◽  
Genetic Fidelity ◽  
Molecular Techniques ◽  
Primary Sequence ◽  
Genetic Expression ◽  
Short Intervals ◽  
Primary Sequence Data

Emperical evidence for intraclonal genetic variation is described here for clonal systems using a variety of molecular techniques and implicating a diversity of mechanisms. However, clonal systems are still generally perceived as having strict genetic fidelity. As concepts of genetic variability move from primary sequence data to include epigenetic and structural influences on genetic expression, the ability to detect changes in the genome at short intervals allows precedence to be given to inherent biological variation that is often analytically ignored. Therefore, the advent of powerful molecular techniques, like genome mapping, mean that our concepts of genetic fidelity within eukaryotic clones and the whole philosophy of the ‘clone’ needs to be re-evaluated and re-defined to replace old unproven dogma in this aspect of science.

scholarly journals New opportunities for designing effective small interfering RNAs

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
James J. Valdés ◽  
Andrew D. Miller
Keyword(s):  
Sequence Data ◽  
Secondary Structures ◽  
Design Guidelines ◽  
Small Interfering Rnas ◽  
Primary Sequence ◽  
Rna Secondary Structures ◽  
Sirna Design ◽  
Adequate Dosage ◽  
Primary Sequence Data

Abstract Small interfering RNAs (siRNAs) that silence genes of infectious diseases are potentially potent drugs. A continuing obstacle for siRNA-based drugs is how to improve their efficacy for adequate dosage. To overcome this obstacle, the interactions of antiviral siRNAs, tested in vivo, were computationally examined within the RNA-induced silencing complex (RISC). Thermodynamics data show that a persistent RISC cofactor is significantly more exothermic for effective antiviral siRNAs than their ineffective counterparts. Detailed inspection of viral RNA secondary structures reveals that effective antiviral siRNAs target hairpin or pseudoknot loops. These structures are critical for initial RISC interactions since they partially lack intramolecular complementary base pairing. Importing two temporary RISC cofactors from magnesium-rich hairpins and/or pseudoknots then kickstarts full RNA hybridization and hydrolysis. Current siRNA design guidelines are based on RNA primary sequence data. Herein, the thermodynamics of RISC cofactors and targeting magnesium-rich RNA secondary structures provide additional guidelines for improving siRNA design.

Molecular characterization of pouched amphistome parasites (Trematoda: Gastrothylacidae) using ribosomal ITS2 sequence and secondary structures

2011 ◽  
Vol 86 (1) ◽  
pp. 117-124 ◽  
Author(s):  
S. Ghatani ◽  
J.A. Shylla ◽  
V. Tandon ◽  
A. Chatterjee ◽  
B. Roy
Keyword(s):  
Sequence Analysis ◽  
Secondary Structure ◽  
Molecular Characterization ◽  
Structure Data ◽  
Sequence Data ◽  
Its2 Sequence ◽  
Primary Sequence ◽  
Sequence Structure ◽  
Interspecific Variations ◽  
Primary Sequence Data

AbstractMembers of the family Gastrothylacidae (Trematoda: Digenea: Paramphistomata) are parasitic in ruminants throughout Africa and Asia. In north-east India, five species of pouched amphistomes, namely Fischoederius cobboldi, F. elongatus, Gastrothylax crumenifer, Carmyerius spatiosus and Velasquezotrema tripurensis, belonging to this family have been reported so far. In the present study, the molecular phylogeny of these five gastrothylacid species is derived using the second internal transcribed spacer (ITS2) sequence and secondary structure analyses. ITS2 sequence analysis was carried out to see the occurrence of interspecific variations among the species. Phylogenetic analyses were performed for primary sequence data alone as well as the combined sequence-structure information using neighbour-joining and Bayesian approaches. The sequence analysis revealed that there exist considerable interspecific variations among the various gastrothylacid fluke species. In contrast, the inferred secondary structures for the five species using minimum free energy modelling showed structural identities, in conformity with the core four-helix domain structure that has been recently identified as common to almost all eukaryotic taxa. The phylogenetic tree reconstructed using combined sequence–structure data showed a better resolution, as compared to the one using sequence data alone, with the gastrothylacid species forming a monophyletic group that is well separated from members of the other family, Paramphistomidae, of the amphistomid flukes group. The study provides the molecular characterization based on primary sequence data of the rDNA ITS2 region of the gastrothylacid amphistome flukes. Results also demonstrate the phylogenetic utility of the ITS2 sequence–secondary structure data for inferences at higher taxonomic levels.

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