Browse Tools

BLAT (BLAST-Like Alignment Tool) is a rapid sequence alignment tool from the UCSC Genome Browser group for aligning mRNA, EST, or DNA sequences to a reference genome. Optimized for highly similar sequ

bedToBigBed — UCSC Kent utility that converts BED/BED+ text files into indexed binary BigBed (.bb) format for fast random-access genome browser tracks. Supports BED3 through BED12, BED+N extra-field e

bigWigMerge merges multiple bigWig signal tracks into a single bedGraph output by summing (or optionally taking the maximum of) per-base signal values. Essential for combining ChIP-seq, ATAC-seq, RNA-

bedGraphToBigWig converts bedGraph coverage files to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-seq, and WGBS coverage tracks.

wigToBigWig converts Wiggle (.wig) format files — fixedStep and variableStep — to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-s

chainTools (UCSC Kent utilities) — command-line suite for manipulating genome pairwise alignment chain and net files produced by LASTZ, BLAT, and other whole-genome aligners. Use when users need to so

bigBedToBed converts bigBed binary indexed files (.bb) back to plain-text BED format. Part of the UCSC Kent utilities (Jim Kent tools). Use when extracting genomic intervals from bigBed files for down

pslMap and pslFilter are UCSC Kent utility programs for manipulating PSL (BLAT alignment) files. pslMap remaps PSL alignments from one coordinate space to another using a chain or mapping PSL file — u

UCSC Kent Utilities — command-line toolkit for genome coordinate conversion (liftOver), binary genome formats (.2bit, BigBed, BigWig), BLAT alignment, annotation format interconversion (GTF↔GenePred),

UCSC Table Browser API — programmatic access to the UCSC Genome Browser's track data via REST endpoints. Retrieve genomic sequences, annotation tracks, gene models, conservation scores, and regulatory

UCSC Track Hub Tools — Kent utilities for building, validating, and hosting custom genome annotation track hubs for UCSC Genome Browser, Ensembl, and WashU Epigenome Browser. Converts BED/wiggle/bedGr

twoBitToFa / faToTwoBit — UCSC Kent utilities for converting between the compact binary .2bit genome format and FASTA. twoBitToFa extracts sequences (full genome or specific regions) from a .2bit file

In-silico PCR (isPCR) simulates PCR amplification computationally by searching a genome or sequence database for products defined by primer pairs. Use for primer specificity checking, amplicon predict

overlapSelect — UCSC Kent utilities command-line tool for filtering genomic records based on coordinate overlap. Selects (or excludes) records from a BED, PSL, genePred, or tab-delimited input file wh

UCSC Genome Browser — web-based genome annotation browser providing access to reference genome assemblies, gene predictions, comparative genomics, variation, regulation, and expression data across hun