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 to navigate the NCBI gene database, perform gene searches for Homo sapiens, and interpret results using boolean operators, accession numbers, and gene location details.

Explore the lactase gene LCP in Homo sapiens, gene ID 3938, with HGNC and Ensembl data, its protein coding status, expression data, reference sequence, and chromosome 2 location in GRCh38.p13.

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

Explore the fasta format data structure, how fasta files store biological sequences, and how to create and view fasta and GenBank files using NCBI resources.

Learn the differences between the faster format and GenBank format, and how GenBank provides comprehensive sequence annotations from NCBI, including accession numbers, descriptions, and CDS features.

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 NCBI homology database and gene families defined by shared ancestry across species. Download homologous genomic datasets, view them in fasta format, and prep for phylogeny analysis.

Learn how to use the ORF finder to search DNA sequences, identify potential open reading frames and coding sequences, check their locations and frames, and download results for analysis.

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.

Learn how to navigate the NCBI genome database and FTP to retrieve genomes, assemblies, annotations, and protein and CDS files in formats like GenBank, GFA, and FASTA for downstream analysis.

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.

Explore the ADA gene region on chromosome 20 with tracks, custom data, and primer design; preview the alternate assembly region around the lactase gene on chromosome 2.

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.

Access the NCBI database of single nucleotide polymorphisms (SNPs) to study human SNPs in coding and noncoding regions, including synonymous, missense, and nonsense mutations and their molecular consequences.

Explore the SNP database, filter by clinical significance to pathogenic variants, and review accession IDs, genomic positions, and gene consequences such as stop gained to understand variant impact.

Explore the dbSNP database in NCBI to access SNP variation data and view genomic placements. Examine clinical significance and pathogenicity, use filters across assemblies, and review frequency with PubMed links.

Explore the dbVAR database of variation to identify structural variations larger than 50 base pairs in the human genome, including insertions, deletions, duplications, inversions, translocations, and complex rearrangements.

Explore the DbVAR database in SCBA to filter human translocation variants, review study details and accession numbers, and download variant calls and sample data for analysis.

Explore the ClinVar database on NCBI, learn to search by gene or specific variant, apply filters for pathogenic interpretations, and use the variation viewer for genomic context.

Explore ClinVar's genome browser and filters to narrow variants, view clinical significance, and link to specific records, while searching diseases like cystic fibrosis or seizures and downloading data for analysis.

Explore ClinVar by searching the cardiomyopathy phenotype, identify pathogenic variants from multiple submitters, and review molecular consequences and cross-references across genes and isoforms.

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 MedGen, a free reference for genetic phenotypes, retrieving disease and gene records, clinical features, patient resources, guidelines, trials, and available genetic tests via advanced search.

Explore MedGen database 2 to search by clinical features, view disease records with integrated descriptions, and access tests, causative genes, and related clinical resources.

Explore the genetic testing registry (GTR) in NCBI, learn to search by conditions, genes, or labs, and navigate tests, labs, and gene links with advanced search tips.

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.

Explore the bio sample database of NCBI, learn to search and filter by organism and sample type, view accession IDs, and access genome sequencing and raw sequence data.

Explore the NCBI SRA database, a public repository for sequencing reads and metadata, and learn to search, filter by organism and platform, download data, and analyze metagenomics for reproducible research.

Explore gene expression and regulation, noting development, disease state, and environment, and identify regulatory elements such as enhancers and promoters plus DNA methylation and chromatin structure that govern transcription.

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 the GEO database, a public functional genomic data repository for gene expression data, including next-generation sequencing and microRNA datasets. Learn to query, download, and analyze expression profiles and studies.

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 GEO profiles, a NCBI resource for storing and querying gene expression data from microarray and high-throughput studies; search by keywords, symbols, or accession numbers to identify differential expression profiles.

Explore the sub databases of GEO, including samples, datasets, GEO profiles, and platforms, and learn how a sample record uses a unique GSM accession to describe condition, manipulations, and abundances.

Learn about geo profiles, datasets, and platforms in the Gene Expression Omnibus. Understand how samples are organized, normalized, and searchable through platform accessions.

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.

Explore GEO series data from the NCBI database, access CDS records, link samples to a single platform, and download data in soft formatted, minimal formatted, and CDS Metrix formats.

Explore gene expression in GEO datasets, where a dataset collects biologically and statistically comparable samples from a single platform with consistent processing.

Learn to choose a suitable GEO dataset for a biology research project by evaluating relevance to your focus, organism, sample size, and current publication date on the NCBI platform.

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.

Learn how to search the NCBI protein database for insulin, filter by species (Homo sapiens), explore databases and data fields, view accession numbers, FASTA formats, and download sequences.

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 to retrieve sequences, run protein blast, and identify conserved domains using the conserved domain database in NCBI, including viewing domain structures and 3D representations of human prion protein.

Learn how the conserved domain search analyzes blast results, identifies putative conserved domains in the prion protein, and compares query and database sequences to reveal domain hits.

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

Learn to run a protein blast search, selecting databases and algorithms, and interpret local alignments, identity, gaps, and taxonomy to assess homology.

Choose the database for protein blast by matching query to non redundant protein sequences, reference proteins, model organisms, curated protein sequence database, PDB, metagenomics, and transcriptome shotgun assembly proteins.

Learn how to choose the right blast algorithm from general blast, psi-blast, and delta-blast, understanding word-based matching, position-specific scoring, conservation, and domain-enhanced searches.

Explore nucleotide blast basics in the NCBI toolkit by selecting databases, configuring algorithms like megablast, and refining results with word size and target sequence settings.

Learn to select nucleotide blast databases in NCBI, including nr/nt, reference sequences, whole genome shotgun, EST, SRA, TSA, patent sequences, PDB archive, and GenBank, with taxonomic context and annotation tips.

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 configure primer blast 2 to limit genomic DNA amplification by setting a base pairs range (min 200 bp) and organism (9606), then run and interpret results.

Explore primer design using primer blast, interpreting graphic and sequence views, primer binding, product length, melting temperature, GC content, and contamination checks for reliable pcr primers.

Explore multiple sequence alignment with Cobalt, identifying conserved regions and shared homology to characterize protein families, derive consensus sequences, and build sequence fingerprints.

Explore how to perform a multiple sequence alignment with the Cobalt tool on the NCBI site, from protein search to blast results, alignments, and a phylogenetic tree.

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.

Explore PubChem, an open NIH chemistry database, cataloging molecules with standardized structures, properties, biological activities, and toxicity, and organizing them into substances, compounds, bioassays, targets, literature, and pathways.

Explore PubMed, the NCBI literature search engine, and master filtering by keywords, boolean operators, and options like abstract, full text, date, and article type.

Explore the NCBI taxonomy database to view taxonomic data, organism names, and lineages for nucleotide and protein sequences, search by ID, browse model and extinct organisms, and inspect genetic codes.

Explore the UCSC genome browser to retrieve genomic information for any species, using web-based tools to view genomes at any scale with annotated data, browse species, and download assemblies.

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.

Explore the table browser tool to extract and analyze bioinformatics data from NCBI, empowering beginners to retrieve tables, filter results, and integrate findings into research workflows.

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 visualize the SARS-CoV-2 genome in a genome browser, set assembly and parameters, zoom into regions, and inspect gene data and GC content.

Explore Ensembl, a vertebrate genome browser that provides annotated gene data, comparative genomics, and regulatory insights, with tools like biomart, blast, and the variant effect predictor for cross-species research.

Learn how to retrieve genes from genomic regions using a central database, explore gene pages, view chromosome location, and visualize transcripts and annotations.

Explore how to locate a gene’s protein and chromosome region in the central database, view splice variants, compare transcripts, and download sequences in multiple formats for analysis.

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.

Explore gene analysis and annotation by querying a gene in a species, exploring comparative genomics, performing alignments, and interpreting gene trees for duplications and speciation.

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

Explore how to access and analyze genomic variation data using the genome browser, filter by variant type and disease phenotype, and view variant locations and gene information.

Learn variation analysis part 2 by navigating the radiation database to identify and analyze variants, view transcript-level evidence, apply filters, and assess predicted consequences and the phenotypic relationships across transcripts.

Explore Ensembl blast to compare a dna or protein query against multiple species. Identify local similarity, view alignments, and inspect genomic locations and gene overlaps.

Explore the Ensembl regulation tool to analyze BRCA2 gene regulation in human, using regulatory builds, transcription factors, open chromatin, and regulatory elements to view regions, phenotypes, and genomic context.

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