BMT

BMT provides integrated analysis of DNA and protein sequences including NGS read trimming, gene prediction by homology, six-frame translation, physiochemical property calculations, pairwise and multiple alignments, and phylogenetic tree generation.

Key Features:

• FastqTrimmer: Performs trimming of low-quality sequences from next-generation sequencing (NGS) reads to improve downstream analyses.
• Gene Prediction: Predicts genes in novel genomes based on homology with reference sequences.
• DNA Analysis: Calculates physiochemical properties of nucleotide sequences.
• Translation: Translates DNA sequences into six open reading frames (ORFs).
• Protein Analysis: Assesses physiochemical properties of protein sequences.
• Pairwise Alignment: Performs global and local pairwise alignments of DNA and protein sequences using multiple substitution matrices.
• Multiple Alignment: Aligns multiple sequences and generates a phylogenetic tree.

Scientific Applications:

• Genomic annotation: Supports annotation of genomes through gene prediction and sequence translation.
• Comparative genomics: Enables sequence comparison via pairwise and multiple alignments.
• Structural biology: Provides protein physiochemical property data relevant to structural and functional analyses.
• Evolutionary studies: Generates phylogenetic trees and supports sequence conservation analysis.

Methodology:

Implemented using Python packages and libraries.