scholarly journals Conserved Motifs and Domains in Members of Pospiviroidae

Cells ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 230
Author(s):  
Kevin-Phil Wüsthoff ◽  
Gerhard Steger
Keyword(s):  
Secondary Structure ◽  
Pairwise Alignment ◽  
Functional Domains ◽  
Alignment Method ◽  
Conserved Motifs ◽  
Fixed Domain ◽  
Original Hypothesis ◽  
The Family

In 1985, Keese and Symons proposed a hypothesis on the sequence and secondary structure of viroids from the family : their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different viroids infecting the same cell and subsequent mutations within each domain”; this article is one of the most cited in the field of viroids. Employing the pairwise alignment method used by Keese and Symons and in addition to more recent methods, we tried to reproduce the original results and extent them to further members of which were unknown in 1985. Indeed, individual members of consist of a patchwork of sequence fragments from the family but the lengths of fragments do not point to consistent points of rearrangement, which is in conflict with the original hypothesis of fixed domain borders.

scholarly journals ncDLRES: a novel method for non-coding RNAs family prediction based on dynamic LSTM and ResNet

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Linyu Wang ◽  
Xiaodan Zhong ◽  
Shuo Wang ◽  
Yuanning Liu
Keyword(s):  
Secondary Structure ◽  
Sequence Alignment ◽  
Short Term Memory ◽  
Homologous Sequence ◽  
Alignment Method ◽  
Consensus Secondary Structure ◽  
The Family ◽  
Novel Method ◽  
Non Coding Rnas ◽  
Structure Annotation

Abstract Background Studies have proven that the same family of non-coding RNAs (ncRNAs) have similar functions, so predicting the ncRNAs family is helpful to the research of ncRNAs functions. The existing calculation methods mainly fall into two categories: the first type is to predict ncRNAs family by learning the features of sequence or secondary structure, and the other type is to predict ncRNAs family by the alignment among homologs sequences. In the first type, some methods predict ncRNAs family by learning predicted secondary structure features. The inaccuracy of predicted secondary structure may cause the low accuracy of those methods. Different from that, ncRFP directly learning the features of ncRNA sequences to predict ncRNAs family. Although ncRFP simplifies the prediction process and improves the performance, there is room for improvement in ncRFP performance due to the incomplete features of its input data. In the secondary type, the homologous sequence alignment method can achieve the highest performance at present. However, due to the need for consensus secondary structure annotation of ncRNA sequences, and the helplessness for modeling pseudoknots, the use of the method is limited. Results In this paper, a novel method “ncDLRES”, which according to learning the sequence features, is proposed to predict the family of ncRNAs based on Dynamic LSTM (Long Short-term Memory) and ResNet (Residual Neural Network). Conclusions ncDLRES extracts the features of ncRNA sequences based on Dynamic LSTM and then classifies them by ResNet. Compared with the homologous sequence alignment method, ncDLRES reduces the data requirement and expands the application scope. By comparing with the first type of methods, the performance of ncDLRES is greatly improved.

In silico, Physico-chemical characterization and analysis of Sandalwood proteins

2018 ◽  
Vol 3 (02) ◽  
pp. 150-157
Author(s):  
Asad Amir ◽  
Neelesh Kapoor ◽  
Hirdesh Kumar ◽  
Mohd. Tariq ◽  
Mohd. Asif Siddiqui
Keyword(s):  
Secondary Structure ◽  
In Silico ◽  
Chemical Characterization ◽  
In Silico Analysis ◽  
Chemical Parameters ◽  
Physico Chemical ◽  
In Silico Studies ◽  
The Family ◽  
Silico Analysis

Sandalwood is a commercially and culturally important plant species belonging to the family Santalaceae and the genus Santalum. In Indian sandalwood is renowned for its oil, which is highly rated for its sweet, fragrant, persistent aroma and the fixative property which is highly demanded by the perfume industry. For better production and varieties, requires to understanding the functions of proteins, their analysis and characterization of proteins sequences and their structures, their localizations in cell and their interaction with other functional partner. Due to limited number of in silico studies on sandalwood, in the present study we have performed in silico analysis by characterization of sandalwood proteins. Total 23 proteins were obtained and characterization using UniProtKB, identifying their physico-chemical parameters using ProtParam tool and prediction of their secondary structure elements using GOR of all 23 proteins.

scholarly journals Comprehensive Secondary Structure Elucidation of Four Genera of the Family Pospiviroidae

PLoS ONE ◽  
2014 ◽  
Vol 9 (6) ◽  
pp. e98655 ◽  
Author(s):  
Tamara Giguère ◽  
Charith Raj Adkar-Purushothama ◽  
Jean-Pierre Perreault
Keyword(s):  
Secondary Structure ◽  
Structure Elucidation ◽  
The Family

scholarly journals Uncovering of Cytochrome P450 Anatomy by SecStrAnnotator

2020 ◽  
Author(s):  
Adam Midlik ◽  
Veronika Navrátilová ◽  
Taraka Ramji Moturu ◽  
Jaroslav Koča ◽  
Radka Svobodová ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Cytochromes P450 ◽  
Specific Protein ◽  
Protein Family ◽  
Homologous Proteins ◽  
Functional Relationships ◽  
Biotransformation Enzymes ◽  
The Family ◽  
Family Based ◽  
Typical Length

AbstractMotivationProtein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of homologous structures and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, assigning always the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs and their variability provides an overview of the studied protein family and can be used to enrich the analysis of a particular protein at hand.ResultsWe developed a workflow for analysis of the secondary structure anatomy of a protein family, based on SSE annotation tool SecStrAnnotator. We applied this analysis to the model family of cytochromes P450 (CYPs) – a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, as well as the conservation/variability of these properties. We also suggest a generic residue numbering scheme for the CYP family. The comparison between the bacterial and eukaryotic part of the family highlights the major differences and reveals an anomalous group of bacterial CYPs with some typically eukaryotic features. This hints at possible evolutionary and functional relationships.AvailabilityThe software and data are available at https://webchem.ncbr.muni.cz/Wiki/[email protected], [email protected]

Secondary structure, high variability and conserved motifs for domain III of 12S rRNA in the Arthropleona (Hexapoda; Collembola)

2004 ◽  
Vol 13 (6) ◽  
pp. 659-670 ◽  
Author(s):  
A. Carapelli ◽  
F. N. Soto-Adames ◽  
C. Simon ◽  
F. Frati ◽  
F. Nardi ◽  
...  
Keyword(s):  
Secondary Structure ◽  
High Variability ◽  
12S Rrna ◽  
Conserved Motifs ◽  
Domain Iii

scholarly journals Multigene-Based Analyses of the Phylogenetic Evolution of Oligotrich Ciliates, with Consideration of the Internal Transcribed Spacer 2 Secondary Structure of Three Systematically Ambiguous Genera

2013 ◽  
Vol 12 (3) ◽  
pp. 430-437 ◽  
Author(s):  
Jiamei Li ◽  
Weiwei Liu ◽  
Shan Gao ◽  
Alan Warren ◽  
Weibo Song
Keyword(s):  
Secondary Structure ◽  
Phylogenetic Trees ◽  
Internal Transcribed Spacers ◽  
Morphological Data ◽  
Its2 Region ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Content Type ◽  
Ssu Rrna Gene ◽  
The Family

ABSTRACT Oligotrichs are ciliates of great abundance, but their molecular systematics are rarely studied. In this study, nine species representing three genera ( Strombidium , Novistrombidium , and Omegastrombidium ) of marine oligotrich ciliates were collected from coastal waters of China. The small subunit (SSU) rRNA gene of two species and the internal transcribed spacers and 5.8S region (ITS1-5.8S-ITS2) for all nine species were sequenced for the first time. Phylogenetic trees using both the SSU rRNA gene and ITS1-5.8S-ITS2 region sequences were generated. In addition, the secondary structures of ITS2 RNA transcripts of 11 taxa representing four genera ( Novistrombidium , Strombidium , Omegastrombidium , and Laboea ) were investigated. The phylogenetic analyses show that (i) the family Strombidiidae is polyphyletic, (ii) the genus Novistrombidium is probably paraphyletic, containing at least two subclades, which is consistent with recent cladistic analyses based on morphological data, and (iii) the tail-less genus Laboea is separate from other genera of Strombidiidae, clustering instead with the tontoniids. Comparisons of the secondary structure of ITS2 regions also show that Laboea is clearly different from other strombidiids. These findings cast doubt on the monophyly of the family Strombidiidae.

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