scholarly journals Study of Essential Sequence Analysis Tools in Bioinformatics : A Brief Overview

2021 ◽  
Author(s):  
Ghafran Ali ◽  
Kanza Ashfaq
Keyword(s):  
Nucleic Acid ◽  
Sequence Analysis ◽  
Protein Sequence ◽  
Consensus Sequence ◽  
Local Region ◽  
Local Alignment ◽  
Global Alignment ◽  
Analysis Program ◽  
Entire Duration ◽  
Essential Sequence

Sequence analysis program is outlined that analyzes and investigates homology between various nucleic acid or protein sequence. The dot matrix technique compares the sequences and the consensus sequence is obtained by superimposing on each other all the dot matrices. Local Alignment and Global Alignment both sequence from start to end is the best possible alignment over the entire duration between the two sequences. This method is more important to align with two closely related sequences roughly the same length. This method may not able to generate optimal results for divergent sequences and variable length sequence because between the two sequences it does not recognize very similar local region.

scholarly journals Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins

2021 ◽  
Vol 22 (5) ◽  
pp. 2647
Author(s):  
M. Quadir Siddiqui ◽  
Maulik D. Badmalia ◽  
Trushar R. Patel
Keyword(s):  
Nucleic Acid ◽  
Nuclear Export ◽  
Consensus Sequence ◽  
Nuclear Export Signal ◽  
Bioinformatic Analysis ◽  
Nucleic Acid Binding ◽  
Protein Protein Interaction ◽  
Lim Domains ◽  
Protein Nucleic Acid ◽  
And Function

Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share similarities with transcriptional regulators and have positively charged electrostatic patches, which may indicate that they have previously unanticipated nucleic acid binding properties. Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3. Furthermore, we analyzed protein expression and mutational frequency in various malignancies, as well as mapped protein-protein interaction networks they are involved in. Overall, our comprehensive bioinformatic analysis suggests that these proteins may play important roles in mediating protein-protein and protein-nucleic acid interactions.

Sign in / Sign up

Export Citation Format

Share Document