This track is part of the MaveDB track collection. It shows where the sequence each MaveDB experiment tested (its "target") lies on the genome: a protein, a coding DNA sequence, or a promoter, enhancer or minigene. Only targets of score sets shown in the MaveDB Heatmaps track are included, and score sets that describe their variants directly on a reference transcript have no target sequence to show.
There are two subtracks, one for DNA targets and one for protein targets, each set to appear only where it has an alignment in view. DNA alignments carry their sequence, so bases that differ from the genome are highlighted; many coding targets are codon optimized for the assay, and those differences are real, not alignment errors. Protein alignments are drawn codon by codon and carry no sequence, so they show where the protein lies but not where it differs.
Each target is placed at the locus where its score set's variants were placed, never by a genome-wide best match. A protein target, or a DNA target that encodes a protein, is matched to the reference protein its variants were placed on, or failing that to another RefSeq protein of the same gene at that locus (another isoform), by the same rule used for the variants: every amino acid must agree at one position, or all but one, or all but a few added at one end. Each amino acid of the target is then drawn on its codon in the genome, so the alignment follows the gene's exons. Other DNA targets, and coding targets that do not match, were aligned to the genome with BLAT (-stepSize=5 -repMatch=2253 -minScore=20 -minIdentity=0), and the best-scoring alignment that overlaps the score set's placed variants was kept. A target with no such alignment is not shown.
The target sequences were downloaded with the score sets from the MaveDB API (https://api.mavedb.org/api/v1, documented at api.mavedb.org/docs). The steps are in the makeDoc file and the scripts in the MaveDB update directory of our source tree.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=mavedb_align_dna or track=mavedb_align_aa.
For automated download and analysis, the alignments are stored in bigPsl files that can be downloaded from our download server. The files are called mavedbAlignDna.bb and mavedbAlignAa.bb. Individual regions or the whole files can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/maveDB/mavedbAlignAa.bb -chrom=chr17 -start=7660000 -end=7690000 stdout
Arbesfeld JA, Da EY, Stevenson JS, Kuzma K, Paul A, Farris T, Capodanno BJ, Grindstaff SB, Riehle K, Saraiva-Agostinho N et al. Mapping MAVE data for use in human genomics applications. Genome Biol. 2025 Jun 25;26(1):179. PMID: 40563119; PMC: PMC12188674
Rubin AF, Stone J, Bianchi AH, Capodanno BJ, Da EY, Dias M, Esposito D, Frazer J, Fu Y, Grindstaff SB et al. MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays. Genome Biol. 2025 Jan 21;26(1):13. PMID: 39838450; PMC: PMC11753097