Understanding Bioinformatics File Formats: From FASTA to GTF INTRODUCTION In the era of big data and high-throughput technologies, bioinformatics has emerged as an indispensable field that bridges biology with computational science. At the core of every bioinformatics workflow—be it genome assembly, variant discovery, transcriptome analysis, or epigenetic mapping—lies one critical element: bioinformatics file formats . These formats serve as standardized containers for biological data, enabling researchers to store, share, analyze, and interpret a wide array of omics datasets across diverse platforms and tools. Each format encapsulates specific types of biological information. For instance, FASTA files store nucleotide or protein sequences; FASTQ files include raw sequencing reads along with quality scores; SAM/BAM files handle sequence alignments; VCF files represent genomic variants like SNPs and INDELs; while GFF and GTF files are used for annotating genes and genomic f...
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