scholarly journals Synapomorphic variations in the THAP domains of the human THAP protein family and its homologs

2021 ◽  
Author(s):  
Hiral M. Sanghavi ◽  
Sharmistha Majumdar
Keyword(s):  
Secondary Structure ◽  
Dna Sequences ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Protein Family ◽  
Cellular Functions ◽  
Multiple Sequence ◽  
Future Studies ◽  
Amino Terminal ◽  
Domain Conservation

AbstractThe THAP (Thanatos-associated protein) domain is a DNA-binding domain which binds DNA via a zinc coordinating C2CH motif. Although THAP domains share a conserved structural fold, they bind different DNA sequences in different THAP proteins which in turn perform distinct cellular functions. In this study, we investigate (using multiple sequence alignment, in silico motif and secondary structure prediction) THAP domain conservation within the homologs of the human THAP (hTHAP) protein family. We report that there is significant variation in sequence and predicted secondary structure elements across hTHAP homologs. Interestingly, we report that the THAP domain can be either longer or shorter than the conventional 90 residues and the amino terminal C2CH motif within the THAP domain serves as a hotspot for insertion or deletion. Our results lay the foundation for future studies which will further our understanding of the evolution of THAP domain and regulation of its function.

scholarly journals Synapomorphic variations in the THAP domains of human THAP proteins and their homologs

2021 ◽  
Author(s):  
Hiral Sanghavi ◽  
sharmistha MAJUMDAR
Keyword(s):  
Secondary Structure ◽  
Dna Sequences ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Protein Domain ◽  
Cellular Functions ◽  
Multiple Sequence ◽  
Future Studies ◽  
Amino Terminal ◽  
Domain Conservation

The THAP (Thanatos-associated protein) domain is a DNA-binding domain which binds DNA via a zinc coordinating C2CH motif. Although THAP domains share a conserved structural fold, they bind different DNA sequences in different THAP proteins, which in turn perform distinct cellular functions. In this study, we investigate (using multiple sequence alignment, in silico motif and secondary structure prediction) THAP domain conservation within the homologs of the human THAP (hTHAP) protein family. We report that there is significant variation in sequence and predicted secondary structure elements across hTHAP homologs. Interestingly, we report that the THAP domain can be either longer or shorter than the conventional 90 residues and the amino terminal C2CH motif within the THAP domain serves as a hotspot for insertion or deletion. Our results lay the foundation for future studies which will further our understanding of the evolution of THAP domain and regulation of its function.

QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction

2019 ◽  
Author(s):  
Fabian Sievers ◽  
Desmond G Higgins
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Reference Sequence ◽  
Supplementary Information ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Reference Sequences ◽  
Selection Of

Abstract Motivation Secondary structure prediction accuracy (SSPA) in the QuanTest benchmark can be used to measure accuracy of a multiple sequence alignment. SSPA correlates well with the sum-of-pairs score, if the results are averaged over many alignments but not on an alignment-by-alignment basis. This is due to a sub-optimal selection of reference and non-reference sequences in QuanTest. Results We develop an improved strategy for selecting reference and non-reference sequences for a new benchmark, QuanTest2. In QuanTest2, SSPA and SP correlate better on an alignment-by-alignment basis than in QuanTest. Guide-trees for QuanTest2 are more balanced with respect to reference sequences than in QuanTest. QuanTest2 scores correlate well with other well-established benchmarks. Availability and implementation QuanTest2 is available at http://bioinf.ucd.ie/quantest2.tar, comprises of reference and non-reference sequence sets and a scoring script. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals Speeding up simultaneous alignment and folding of RNA sequences

2014 ◽  
Vol 4 (3) ◽  
Author(s):  
Mária Šimalová ◽  
Gabriela Andrejková
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Secondary Structure Prediction ◽  
Optimal Solution ◽  
Rna Sequences ◽  
Multiple Sequence ◽  
Rna Secondary Structure Prediction ◽  
Folding Algorithm ◽  
Alignment Problem

AbstractIn the paper, we describe and develop more effective solutions of two important problems in bioinformatics. The first problem is the multiple sequence alignment problem and the second problem is RNA secondary structure prediction (folding) problem. Each of these problems should be solved with better results if we know the solution of the other one, but usually we only have sequences and we know neither the alignment nor the secondary structure. Precise algorithms solving both of these problems simultaneously are computationally pretentious according to the big length of RNA sequences. In this paper, we have described the method of speeding up the Sankoff’s simultaneous alignment and folding algorithm using the Carrillo-Lipman approach to cut off those computations, that can never lead to an optimal solution.

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