Genome browser (IGV)

Use a genome browser when you need to see where a ChIP peak sits on a chromosome, inspect variants in a VCF, check coverage over an exon, or sanity-check coordinates before cloning. It complements sequence-level tools on this site such as Promoter Grabber and the TF binding scanner.

We host this page so you can open a familiar IGV-style view without installing the desktop IGV client or leaving the Bond Lab tool hub. Typical jobs include locating TP53 on hg38, loading a small BAM from a pilot RNA-seq run, or overlaying a BED of called peaks next to the reference gene model.

The viewer is built with IGV.js (MIT licence), loaded from jsDelivr. On startup the page fetches the public genome list from igv.org/genomes, matching the configuration used by igv-webapp. Gene search uses IGV’s built-in lookup for supported assemblies (human hg19/hg38, mouse mm10/mm39, and others).

Tracks loaded from your machine stay local — they are read in the browser and not uploaded to thebondlab.net. URL tracks are fetched directly from the host you specify (which may log access). The IGV toolbar inside the white panel supports zoom, pan, and per-track menus as in the official web app.

1. Genome: choose an assembly (default hg38) and click Apply genome.
2. Locus: enter a gene symbol (e.g. MYC, BRCA1) or coordinates (e.g. chr17:43044295-43125483) and click Go.
3. Mark region: click Mark current view to add a red bar for the visible window (above gene exon/intron tracks). Right-click the bar to copy reference sequence.
4. Find motif: enter a DNA pattern with IUPAC codes (e.g. GAATTC, WGATAR), choose search region, and click Find motif. + strand hits load on a teal track; − strand hits on pink.
5. ENCODE TF ChIP: click Browse ENCODE to search released transcription-factor ChIP-seq signal tracks (fold change over control bigWig) for the current assembly.
6. URL track: paste a direct link to a track file. For indexed formats (BAM, CRAM, Tabix VCF/BED), also paste the index URL (.bai, .crai, .tbi).
7. Local track: choose a file and click Load local file. Pair BAM/CRAM with its index if both are required; some formats work without an index for small files.
8. Navigate: use the IGV controls in the viewer panel to zoom, scroll, and manage tracks.

Tip: share a session by copying the page URL after loading tracks — IGV.js can encode state in query parameters when queryParametersSupported is enabled.

Enter a DNA motif using standard IUPAC degeneracy codes. Sense matches (motif on the forward strand) appear on a teal track; antisense matches (reverse complement on the forward reference) appear on a pink track. Examples: GAATTC (exact EcoRI site), WGATAR (TATA-box-like), CCWGG (MspI/HpaII family), NNK (any two bases then G or T).

IUPAC codes: R = A/G · Y = C/T · M = A/C · K = G/T · S = G/C · W = A/T · H = A/C/T · B = C/G/T · V = A/C/G · D = A/G/T · N = any base

• Not the full IGV-Web app. This page covers core browsing, search, and track loading. Features such as Dropbox/Google Drive pickers, session save, and circular view from igv-webapp are not included here; use igv.org/app for those.
• CORS for URL tracks. Remote files must allow cross-origin requests from your browser, or load will fail.
• Large files. Whole-genome BAMs may be slow or exceed browser memory; prefer small regions or subsampled files for quick checks.
• Third-party script. IGV.js is loaded from jsDelivr; if blocked, the viewer will not start.

• Promoter Grabber — fetch promoter DNA 5′ of the TSS from NCBI.
• TF binding scanner — scan DNA sequence for motif hits.
• Cross-species TF scanner — conserved motifs across three promoters.
• Sequence aligner — pairwise or multi-sequence alignment.