# BioSuiteT: A Unified Tool for Biological Sequence Analysis
## 2 Materials and Methods
### Development Framework for BioSuiteT and Modules  
BioSuiteT is built on the Django framework [48], selected for its efficiency in rapid web application development and its support for modular, scalable architectures [49]. Additionally, to store biological data, BioSuiteT uses MongoDB for its high performance in handling a vast amount of information [50]. The main components can be seen in Figure 4, followed by a description of BioSuiteT functionalities and its interfaces. There are several parts of the GUI that, considering its size, cannot be placed completely; for this reason, we have included a Supplementary Material folder that contains a full-size version of each interface that BioSuiteT includes. Below, the key components and functionalities of BioSuiteT are described. 1. DNA Sequence Analysis: 1. Properties analysis: BioSuiteT receives as input a sequence of DNA and, as output, delivers the complementary sequence, reverse complementary sequence, and the distribution of the amino acids with its plot (see Figure 5). Figure 4: Components of BioSuiteT. Figure 5: DNA sequence analysis interface. 2. Protein Sequence Analysis: 1. Properties analysis: BioSuiteT receives as input a sequence of proteins and a pH level for calculating Charge; as output, it delivers the sequence length, molecular weight, aromaticity, instability index, isoelectric point, secondary structure, extinction coefficient, disulfide bridges, hydrophobicity, charge, and plots of amino acid distribution and Kyte Doolittle hydrophobicity (see Figure 6). 3. Transcription and Reverse Transcription: 1. Transcription: Converts nucleotide sequences to mRNA and provides template strands (see Figure 7, left side). 2. Reverse transcription: Converts mRNA back to nucleotide sequences (see Figure 7, right side). 4. Sequence Translation 1. Sequence translation: BioSuiteT receives as input a sequence of mRNA and, as output, delivers the translated amino acid sequence using the respective codon table (BioSuiteT includes all the codon tables; see Figure 8). Figure 8: Translation tool interface. Figure 6: Protein sequence analysis interface (part of the image has been cut due to size). Figure 7: Transcription and back transcription tool interface. * Pairwise Sequence Aligner
* Pairwise sequence aligner: BioSuiteT receives as input two sequences for alignment and, as outputs, delivers aligned sequences with alignment statistics, such as match score, mismatch score, gap score, and information on the type of alignment (local and global). Also, BioSuiteT has all the penalization matrixes (Jones, Levin, McLachlan, MDM78, MegaBlast, NUC 4.4, and 23 more; this can be seen in Figure 9). * BLAST Tool
* Sequence search: BioSuiteT receives as input a sequence of proteins, nucleotides, or genes; as output, it delivers a list of organisms with similar sequences using BLAST (BioSuiteT includes BLAST-N, BLAST-P, T-BLAST-N, and BLAST-X; see Figure 10). * PDB Viewer
* Visualization: BioSuiteT receives as input a PDB file, and as output, a 3D protein structure visualization with multiple modes (sticks, cartoons, spheres, lines, cross, label alpha C's, and variations in surfaces; this can be seen in Figure 11). Figure 10: BLAST tool interface. Figure 9: Sequence aligner tool interface. This interface enables users to align two sequences and select the type of alignment they want to perform, along with the desired penalization matrix. * PDB Analysis
* Properties analysis: BioSuiteT receives as input a PDB file; as output, it delivers the properties of the structure such as structure name, deposition date, release date, structure resolution, structure keywords, structure method, structure reference, journal reference, author, compound, source, missing residues information, glycosylation information, model list, chain list, residues list, atom name and coordinates, \(\beta\) factor, element and atom distribution plots, and hetero atom information (see Figure 12).