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An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
ApicoAlign: an alignment and sequence search tool for apicomplexan proteins
Jamshaid Ali1, Umadevi Paila, Akash Ranjan
1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, A Sun Centre of Excellence in Medical Bioinformatics, Hyderabad 500001, India.
BMC Genomics
|February 29, 2012
Summary
New protein matrices (SMAT80 and PfFSmat60) improve the detection and alignment of apicomplexan proteins, aiding genome annotation. A web tool, ApicoAlign, is now available for this purpose.
Area of Science:
- Bioinformatics
- Genomics
- Proteomics
Background:
- Genome sequencing projects generate vast amounts of data requiring accurate protein annotation.
- Standard protein comparison matrices (e.g., BLOSUM, PAM) may not optimally serve diverse species like those in Apicomplexa.
- Previous work developed Plasmodium falciparum-specific matrices (PfSSM) showing improved performance.
Purpose of the Study:
- To evaluate and extend the utility of parasite-specific substitution matrices for apicomplexan protein annotation.
- To develop a user-friendly web application for aligning and identifying orthologs of apicomplexan proteins.
Main Methods:
- Development and application of novel substitution matrices (SMAT80, PfFSmat60) derived from apicomplexan proteomes.
- Comparative analysis of these matrices against standard matrices (BLOSUM) using non-redundant databases.
- Utilizing the developed matrices in a web server (ApicoAlign) for ortholog detection and protein alignment.
Main Results:
- SMAT80 and PfFSmat60 demonstrate superior performance over BLOSUM for apicomplexan proteins in detecting orthologs and improving alignment quality.
- Significant improvements observed in E-values, bit scores, percent identity, and alignment length.
- Successfully identified orthologs for key proteins (e.g., rhomboid proteases, U2 snRNP auxiliary factor) across different apicomplexan species and even in distantly related organisms like Arabidopsis thaliana.
Conclusions:
- The SMAT80 and PfFSmat60 matrices offer enhanced accuracy for apicomplexan protein analysis compared to existing methods.
- These matrices are valuable tools for improving the annotation and functional characterization of apicomplexan genomes.
- The ApicoAlign web server provides a practical resource for researchers working with apicomplexan protein data.
