# BioSuiteT: A Unified Tool for Biological Sequence Analysis
## 2 Materials and Methods
### Comparison Between Bioinformatics Platforms and Software Tools and Libraries  
Table 1 compares the functionalities offered by each platform, software tool, and library for summarizing information; this table highlights the specific capabilities that each one provides. ExPASy provides a comprehensive suite of bioinformatics tools, offering full support for sequence analysis, structure prediction, homology search, alignments, primer design, gene expression analysis, functional annotation, data retrieval, and processes such as translation and transcription. It includes basic tools for phylogenetic analysis, but these are less advanced than those of other platforms. For genome and species exploration, ExPASy provides access to related databases but lacks the in-depth tools available in platforms like NCBI. Its support for interaction analysis is partial, offering some protein-protein interaction predictions but with limited depth. Similarly, support for variants and mutations is limited, relying primarily on external databases without dedicated tools for detailed analysis. NCBI Tools provides a comprehensive suite of bioinformatics functionalities, encompassing full support for sequence analysis, homology search and alignment, primer design, gene expression analysis, functional annotation, data retrieval, phylogenetic analysis, translation and transcription, genome and species exploration, and analysis of variants and mutations. Structure prediction is partially supported through access to structural data and basic modeling tools, although these are less advanced than those offered by dedicated platforms, such as ExPASy. Structural visualization is also partial, with tools such as Cn3D [44] available for viewing molecular structures but lacking the advanced features found in software like Chimera. Interaction analysis is limited, providing some resources for studying biological interactions, but not as comprehensive as specialized tools. Additionally, NCBI Tools does not support reverse transcription, which restricts its ability to simulate RNA-to-DNA conversion. Chimera is a specialized tool focused on structural visualization and analysis, with full support in this area. It excels at displaying 3D molecular structures of proteins and \begin{table}
\begin{tabular}{c c c c c c c c c c} \hline \hline \multirow{2}{*}{**Functionalities**} & \multicolumn{6}{c}{**Platforms**} & \multicolumn{6}{c}{**Software Tools and Libraries**} \\ \cline{2-10}  & **ExPASy** &
\begin{tabular}{c} **NCBI** \\ **Tools** \\ \end{tabular} & **Galaxy** & **Geneious** & **Benchling** & **UCGENE** & **Chimera** & **BLAST** & **BioPython** \\ \hline Sequence analysis & & & & & & & & Partial & & \\ Structure prediction & & & & & & & & & & Partial \\ Homology search and sequence alignment & & & & & & & & & & \\ Primer design & & & & & & & & & Partial \\ Gene expression analysis & & & & & & & & & Partial \\ Functional annotation & & & & & & & Partial & & Partial \\ Databases and data retrieval & & & & & & & & & Partial \\ Phylogenetic analysis & & & & & & & & & & \\ Structural visualization and analysis & Partial & Partial & & & Limited & & & & & Limited \\ Translation and transcription & & & & & & & & & & & Partial \\ Genome and species exploration & Partial & & & & & & & & Partial \\ Reverse transcription & & & & & & & & & & & Partial \\ Interaction analysis & Partial & Partial & & & & & & & & Partial \\ Variants and mutations & Limited & & & & & & & Partial & Partial \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Comparative table of functionalities among bioinformatics platforms, software tools, and libraries. \(\blacktriangledown\) means a functionality that is covered, \(\blacktriangledown\) means a function that is not covered. “Partial” indicates that the functionality is only partially supported—either limited in scope, applicability, or implementation. “Limited” refers to functionalities that are constrained in performance or usability, or depend heavily on specific conditions, configurations, or external dependencies.