NCBI Mastery- A Beginner's Guide to Bioinformatics

Learn to search NCBI for a Homo sapiens mRNA sequence, filter to nucleotide data and mRNA, and download a complete record while recognizing exon-intron structure and alternative splicing.

Learn to interpret NCBI data in FASTA format, including accession numbers, reference sequences, locus and versioning, sequence length, and key features like coding DNA sequences and translations.

Explore how the LTG gene is analyzed in NCBI, covering genomic context, RNA expression across tissues, phenotypes, pathways, and cross-database references.

Explore GenBank, the NCBI DNA sequence database, and its GenBank and FASTA formats, then learn four retrieval methods: search and download, ftp access, BLAST, and Python-based programmatic retrieval.

Master the NCBI RefSeq database, a non-redundant resource for genomic, transcript, and protein data. Learn to access, download fasta transcripts, and search the RefSeq gene database for non-redundant gene data.

Explore the genome database to retrieve genomes from public-domain organisms, including sequences, chromosomes, assemblies, and annotations, using organism browse, filters, and FTP downloads.

Discover how to retrieve Gallus gallus genomes from the public domain, interpret the genome homepage, download sequences and annotations in fasta and GenBank formats, and perform BLAST analyses.

Explore the NCBI genome database to retrieve and analyze the Gallus gallus chicken genome, view chromosome structures, download GenBank files, and search by gene ID.

Explore the NCBI genome data viewer to browse assemblies, search organisms via a phylogenetic tree, and view chromosomes in an ideogram view, with download options.

navigate the main browser interface of the genome data viewer, explore the human assembly with the exon navigator on chromosome one, and customize with user data and track hubs.

Learn how genome assembly combines overlapping short reads to produce a complete genome, explore assembly levels from scaffolded to chromosomes, and download fully sequenced assemblies from the NCBI genome database.

Explore the Genome Reference Consortium, a research network that updates human, mouse, zebrafish, and chicken genome assemblies, fixes errors with patches, and provides downloadable ftp data.

Explore the OMIM database to search human genes and their associated disorders using advanced search, clinical synopsis, and gene maps, with links to NCBI resources.

Explore the Biosystems database, which integrates biological systems data to link proteins, genes, and small molecules to metabolic pathways and higher functions, emphasizing manually curated pathways.

Navigate the NCBI bio project database to access a centralized, hyperlinked collection of genome data for a given organism or project, and download related datasets.

Learn gene expression via microarray, from RNA labeling and hybridization to data analysis, and explore the gene expression omnibus (GEO) for datasets linking regulation, variation, disease prevention, and biotech uses.

Explore how the GEO database stores high-throughput genomic data, enables simple submissions, and provides user-friendly access to studies and gene expression profiles.

Explore gene expression samples in GEO, including GSM accession numbers and platform links, and learn how sample records connect CDS and series to datasets via the GEO repository.

Learn to access gene expression data in GEO samples, review sample records, and navigate platforms and CDs that link multiple samples for a research focus.

Learn how to locate and filter glioma datasets in GEO, set human as the organism, apply sample-count filters, read dataset synopses, and evaluate data freshness and sample size before downloading.

Learn how GEO platforms define datasets with GPL accession numbers, covering technologies from high-throughput sequencing to microarrays, and how multiple samples merge into a single platform acquisition.

Explore gene expression profiles in GEO, access the dataset browser, and download expression data across samples to understand the end-to-end pipeline from curated datasets to profiles.

Explore GEO profiles and platform numbers to locate series, references, and six mouse samples; analyze differential expression, download data, and visualize expression density and mean-variance trends.

GEO2R 1 teaches you to use the NCBI GEO2R tool to compare gene expression between control and major depressive disorder groups, analyze microarray data, and interpret p-values for dataset significance.

Explore GEO2R 2 to analyze differential expression between control and MDT groups, interpret p-values, log fold change, and top genes through plots and downloadable data.

Explore mmdb, the ncbi molecular modeling database, offering experimentally resolved 3d structures of dna and rna from the protein databank, with tools to view, analyze domains, and download structures.

Learn protein blast basics, global vs local alignment, and how to compare sequences against databases to identify homologous, conserved functional regions.

Blastx translates a nucleotide query and searches a protein database to identify regions of local sequence similarity, presenting hits with scores, identities, frames, and e-values.

Explore protein to translated nucleotide blast (tBLASTn) to identify homologous genes by comparing a query sequence against a nucleotide database, with attention to word size, expect threshold, and scoring matrices.

Design real-time PCR primers for human interleukin-6 using NCBI Primer-BLAST, choosing the full transcript and applying product size, melting temperature, and junction inclusion constraints.

learn to build phylogenetic trees by comparing sonic hedgehog protein sequences across species, download and curate sequences, perform sequence alignment and blast comparisons, and infer evolutionary relationships.

Compare the human sequence with other species to build a phylogeny tree and interpret alignment scores and percentage identity. Explore distance trees, common ancestors, and layout options to reveal relationships.

Learn to retrieve an entire genome with a genome browser, download sequence and annotation data, and use command-line tools and Visual Studio Code for analysis.

Retrieve the SARS-CoV-2 genome and its annotations using the table browser, then compare sequence, bed, and browser-extensible data formats to identify gene locations and CDS details.

Learn to retrieve a genome assembly with the symbol genome browser, selecting a species like polar bear, then access assembly details, gene annotation, comparative genomics, and download fasta sequences.

Perform gene analysis and annotation, compare genomes, build phylogenetic insights, and explore variants, ontologies, and pathways to interpret gene function.

Use the Ansible comparative genomics tool to download and analyze vertebrate genome alignments, including homology, multiple alignments, and coding DNA, protein, and RNA sequences.