리서치·학습 스킬

Align multiple protein sequences with EBI Clustal Omega and save the results locally. Compare sequence identity, examine conserved regions that remain unchanged across proteins, and map known functional residues to corresponding positions in the alignment.

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• Comparing multiple protein sequences
• Checking conservation of known functional residues
• Comparing a protein fragment with a full-length sequence

Retrieve evolutionary conservation scores and transcription factor binding sites from UCSC Genome Browser. Examine how genomic positions have changed across species and locate sites where gene-regulating proteins may bind, supporting analysis of variants and regulatory regions.

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• Checking conservation at single-nucleotide variants
• Finding conservation peaks across regulatory regions
• Looking up transcription factor binding sites in a region

Search PubMed for biomedical papers and published clinical trials, retrieve abstracts and open-access full text, and connect papers with gene or compound records. Resolve incomplete citations and retrieve larger sets of references in batches.

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• Find biomedical papers and published clinical trials
• Retrieve abstracts and open-access full text
• Explore papers linked to specific genes or compounds

Query QuickGO to connect genes with biological processes, molecular functions, and cellular locations. Find genes linked to a functional term, explore relationships between terms, and check the evidence supporting each annotation.

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• Look up a gene’s functions
• Find genes associated with a GO term
• Explore definitions and relationships of GO terms

Query STRING to find protein interaction partners, examine supporting evidence and confidence scores, and identify biological pathways overrepresented in a protein list. It also supports homology searches and enrichment analysis using ranked experimental measurements.

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• Finding interaction partners for a protein
• Checking interaction evidence and confidence scores
• Identifying pathways overrepresented in a protein list

Find datasets of direct interactions between DNA and transcription factors, proteins that regulate gene activity, in UniBind. Filter by species, cell line, or factor name, inspect dataset details, and download binding sites as BED or FASTA files.

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• Find binding datasets for a transcription factor
• List datasets for a species or cell line
• Inspect dataset details and data sources

Search open-access life-science literature in Europe PMC by keyword, author, or article identifier. Download available PDFs and full texts as plain text or XML, and retrieve reference lists and papers that cite a study.

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• Find open-access papers on a life-science topic
• Look up a paper by DOI or PMID
• Save full text as PDF, plain text, or XML

Look up human genetic variants in ClinVar to retrieve disease-related classifications, review status, associated conditions, and evidence from submitting laboratories. Compare conflicting interpretations or find variants classified as pathogenic for benchmark controls.

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• Checking a variant's disease-related classification
• Comparing interpretations from different laboratories
• Finding pathogenic variants for benchmark controls

Retrieve protein and nucleotide sequences from NCBI using accession numbers, gene names, organisms, locus tags, PubMed articles, or patent numbers. Translate coding regions into protein sequences and search by organism and expected length when other identifiers are unavailable.

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• Retrieving sequences by accession number
• Finding proteins by gene name or locus tag and organism
• Collecting protein sequences linked to papers or patents

Retrieve preprint metadata from bioRxiv and medRxiv using a known DOI or a short date range and subject category. Filter results by keywords or author, optionally include abstracts, and save the matching records as JSON.

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• Retrieving paper metadata from a known DOI
• Reviewing preprints from a specific period and subject
• Filtering a short period by keywords or author

Explore disease-associated genes and known drugs using Open Targets Platform. Retrieve genetic evidence, predictions linking variants to genes, and information on whether a target can be addressed by drugs, including available safety data.

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• Find target genes associated with a disease
• Review druggability and safety information for a target
• Look up drugs and clinical candidates for a disease

Explore ENCODE data to find candidate DNA regions that regulate gene activity. Retrieve cell-specific annotations, nearby or linked genes, gene expression measurements, and experiment or file records, including ChIP-seq peaks, through the supplied scripts.

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• Finding candidate regulatory regions at genomic coordinates
• Checking genes near or linked to a regulatory region
• Comparing gene expression across biosamples

Look up human proteins in the Human Protein Atlas to see their abundance by tissue and location within cells. Retrieve expression levels reported as categories, search for matching genes, and compare protein findings with RNA expression data.

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• Checking protein abundance across human tissues
• Finding where a protein is located within cells
• Comparing RNA and protein expression

Search RCSB PDB for experimentally determined structures of proteins, nucleic acids, and bound molecules. Find entries by sequence or structural similarity, download atomic coordinate files, and retrieve experimental methods, resolution, and other structure metadata.

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• Find structures with similar sequences or shapes
• Download atomic coordinates in pdb or mmcif format
• Check experimental methods and resolution

Analyze Latin and Ancient Greek inscriptions to restore missing characters, estimate their place and date of origin, and find parallel texts. Review model predictions in tables and an HTML dashboard, with optional numerical text representations for further analysis.

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• Restoring missing characters in ancient inscriptions
• Estimating where and when an ancient text originated
• Finding parallel inscriptions for comparison

Search openFDA for adverse event reports, recalls, labeling, approvals, and other regulatory records covering drugs, devices, foods, and more. Summarize field counts and download matching records as JSON files for further analysis.

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• Search adverse event reports for a drug
• Check recall records for devices or foods
• Look up drug labeling and NDC records

Use AlphaGenome scores to investigate predicted molecular effects of genetic variants, annotate variant files, and rank research candidates. Scan genomic regions for single nucleotide substitutions and retrieve matching gene structures, including exon and splice junction coordinates.

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• Inspecting predicted functional effects of individual variants
• Annotating variant files and ranking research candidates
• Scanning genomic regions for impactful single nucleotide substitutions

Search PubChem by chemical name, identifier, or molecular structure to retrieve properties, hazards, and pharmacology information. Find similar molecules or compounds containing a chosen structural fragment, and retrieve structure images and biological assay data.

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• Checking a compound's properties and alternative names
• Finding molecules with similar structures
• Looking up chemical hazards and handling precautions

Find DNA binding profiles for transcription factors, proteins that regulate genes, in JASPAR. Resolve gene names to matrix IDs, retrieve binding patterns and metadata, and export profiles in formats used by sequence analysis tools.

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• Retrieve DNA binding patterns for a transcription factor
• Resolve gene names to JASPAR matrix IDs
• Convert frequency matrices to binding scores

Look up biomedical terms in EMBL-EBI OLS across more than 250 ontologies, structured vocabularies that connect related concepts. Find definitions, synonyms, and identifiers, then explore broader categories, subtypes, and relationships such as anatomical parts.

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• Check definitions and synonyms of biomedical terms
• Find term identifiers for diseases or gene functions
• Explore broader categories and subtypes

Look up short genetic variants in NCBI's dbSNP database. Connect rsIDs, identifiers for known variants, with genomic coordinates and HGVS variant descriptions, retrieve associated genes and allele frequencies, or search a chromosome region.

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• Find a known variant's rsID from genomic coordinates
• Check associated genes and allele frequencies for an rsID
• Convert an HGVS variant description to genomic coordinates

Search OpenAlex for academic papers, author publications, and institutional research. Look up papers by DOI, a persistent publication identifier, summarize citation data, and download open-access PDFs through the included command-line tool.

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• Find academic papers on a research topic
• List an author's publications
• Look up paper details by DOI

Retrieve AlphaFold protein structures using a UniProt ID and summarize prediction confidence, boundaries of rigid structural regions, and likely disordered regions. Downloaded structure files and error estimates support further examination of the results.

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• Check confidence in a predicted protein structure
• Identify boundaries of rigid structural regions
• Assess regions likely to lack a stable structure

Query gnomAD to check how common genetic variants are overall and across ancestry groups. Retrieve gene constraint scores, which describe intolerance to loss of function, and find variants within a specified gene or genomic region.

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• Checking how rare a genetic variant is
• Comparing allele frequencies across ancestry groups
• Retrieving gene intolerance scores such as pLI and LOEUF