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Description
This track displays alignments of the tested gene sequences for experiments in
MaveDB (see the accompanying heatmap track for
more details). Please note that only a subset of MaveDB experiments could be displayed as
heatmaps; the sequence alignments in this track only cover those experiments.
Display Conventions
There are two subtracks - one for alignments of DNA sequences and one for peptide sequences. For convenience,
the subtracks are set by default to only appear when an alignment appears in the current view window.
The DNA subtrack is also configured to highlight base differences from the reference genome. Due to the
alignment method, this highlighting is currently unavailable for the peptide alignments.
Methods
Sequences from MaveDB experiments were aligned using BLAT. DNA sequences went through two processes.
First they were aligned directly to the genome. Second they were aligned directly to GENCODE transcripts,
and the resulting alignments were projected onto the genome using pslMap (the former method is more likely
to capture intronic matches, while the latter does a better job of capturing the expected exon boundaries).
The two alignment sets were then combined and filtered for overlap with the mapped loci of the corresponding
heatmaps, and the best alignments were selected for presentation.
Two DNA sequences (for 00000002-a-2 and 00000053-a-2) weren't sufficiently identical for this process to
find a good alignment; in those cases, the sequences were instead aligned using BLAT's translated alignment flags.
Peptide sequences went solely through the GENCODE-pslMap path.
Data Access
Direct access to the data files for these experiments can be obtained from
MaveDB.
References
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
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