Tagged bioinformatics

Design protein sequences for a backbone with ProteinMPNN inverse folding NIM

Co-design protein structures and sequences with the RFD4-Proteina NIM

Design protein backbones and binders with RFDiffusion NIM

Negotiate a hostage or execution threat by sequencing terms and buying time

Fetch AlphaFold structures by UniProt ID and read pLDDT confidence scores

Build AlphaGenome Atlas links for variants, loci and prediction views

Analyze how a genetic variant affects gene expression and chromatin with AlphaGenome

Look up SNPs in dbSNP by rsID, VCF coordinates or HGVS strings

Query ENCODE cCRE regulatory elements and ChIP-seq experiment files

Resolve Ensembl gene IDs, fetch sequences and run variant effect prediction

Find proteins structurally similar to your PDB or mmCIF file with Foldseek

Check variant allele frequencies and gene constraint scores in gnomAD

Pull GTEx tissue expression levels and eQTL variant data for genes

Get Human Protein Atlas protein expression and subcellular location data

Find protein domains, families and GO terms with InterPro annotations

Fetch protein and nucleotide sequences from NCBI by accession or gene

Search and download experimental 3D structures from the Protein Data Bank

Align multiple protein sequences with Clustal Omega to check conservation

Find homologous protein sequences with MMseqs2 or BLAST searches

Search PubMed papers and trials and link them to genes and compounds

Render protein structures in PyMOL with alignments and distance measures

Map genes to Gene Ontology terms and explore GO hierarchies with QuickGO

Find protein interaction partners and enrichment with STRING scores

Search UniProt for protein function, taxonomy and sequences

Validate protein designs and binder complexes with AlphaFold2 confidence scores

Fetch AlphaFold predicted protein structures by UniProt ID and read pLDDT scores

Work with AnnData objects and h5ad files for single-cell and omics data

Design protein binders with BindCraft and built in AlphaFold2 validation

Choose between BoltzGen, BindCraft and RFdiffusion for protein binder design

Call open chromatin peaks from ATAC-seq alignments with MACS3

Check ATAC-seq library quality with TSS enrichment, FRiP and fragment sizes

Find differentially accessible chromatin regions between ATAC-seq conditions

Detect transcription factor footprints in ATAC-seq data with TOBIAS

Map nucleosome positions and nucleosome free regions from ATAC-seq fragments

Test whether a GWAS and eQTL signal share one causal variant with coloc

Narrow GWAS loci to likely causal variants with SuSiE and FINEMAP

Estimate causal effects between traits with Mendelian randomization using TwoSampleMR

Preprocess cell free DNA reads with short fragment alignment and UMI dedup

Compare ChIP-seq binding between conditions with DiffBind and replicate samples

Find enriched transcription factor motifs in ChIP-seq peaks with HOMER and MEME

Annotate ChIP-seq peaks to promoters, introns and nearest genes with ChIPseeker

Call narrow and broad ChIP-seq peaks with MACS3 using input controls

Check ChIP-seq quality with FRiP, cross correlation and IDR replicate concordance

Identify super-enhancer domains from H3K27ac ChIP-seq with ROSE

Plot ChIP-seq signal heatmaps, profiles and genome browser tracks

Map rsIDs to genomic coordinates and pull dbSNP variant annotations

Call HLA alleles from sequencing data with OptiType, HLA-HD or arcasHLA

Look up drug gene interactions and dosing guidelines in PharmGKB and CPIC

Annotate copy number calls with affected genes, pathways and clinical notes