HumanBase DeepSEA

DeepSEA analysis
DeepSEA is a deep learning framework that predicts genomic variant effects on a wide range of regulatory features with single nucleotide sensitivity: transcription factors binding, DNase I hypersensitive sites, and histone marks in multiple human cell types.

New sequence model

Sei provides a global map from any sequence to regulatory activities, as represented by 40 sequence classes by integrating predictions for 21,907 chromatin profiles. You can also find the Sei code repository here or read about our manuscript here. See for more details.

Submit a DeepSEA analysis

Model:

Sei (DNA model)

Type:

VCF

Genome assembly:

GRCh37/hg19

Show format descriptions

VCF (Variant effect prediction)

Upload a VCF file for variant effect prediction. VCF format:

Each line must have at least 5 tab separated fields.
If there is a header column, it must begin with a hash `#` and the first 5 tab separated entries must be the following: `#CHROM`, `POS`, `ID`, `REF`, `ALT`
The first column: Chromosome name (hg19). (check hg19 chromosome list)
The second column: Position (hg19). A positive integer within chromosome length. (check hg19 chromosome list)
The third column: Variant name. This field can be left empty.
The fourth column: Reference allele. One or more upper case codes from ATCG. Maximum 100 characters.
The fifth column: Alternative allele. Contain one or more upper case codes from ATCG. Maximum 100 characters.
Required for SeqWeaver - The sixth column: Strand. Either ‘+‘ or ‘-‘ indicating strand.

A VCF file can be opened in any text editor. However, for most users a VCF file is best viewed using a spreadsheet program such as Microsoft Excel or Google Sheets.

Example VCF file
Example VCF file with strand

BED (Chromatin feature prediction)

Upload a BED file for chromatin feature prediction. BED format:

Each line has at least 3 tab separated fields.
The first column: Chromosome name (hg19). (check hg19 chromosome list)
The second column: Start Position (hg19). A non-negative integer within chromosome length. (check hg19 chromosome list)
The third column: End Position (hg19). A non-negative integer within chromosome length.
The difference in values between Start and End Position should be 1000 or less (We only use the center positions. See help page for details).

Example BED file

FASTA (chromatin feature prediction / in-silico mutagenesis)

Upload a FASTA file for chromatin feature prediction or in-silico mutagenesis. FASTA format:

Each section starts with ">".
Sequence length depends on the selected model: Sei (4096bp), Beluga (2000bp), or Seqweaver (1000bp)
Allowed nucleic acid codes: ATCGatcg (lowercase is treated the same of uppercase).

Example FASTA file

File upload Paste contents Example vcf submission

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DeepSEA is a deep learning framework that predicts genomic variant effects on a wide range of regulatory features with single nucleotide sensitivity: transcription factors binding, DNase I hypersensitive sites, and histone marks in multiple human cell types.

Visitfor addtional help and details.

Flatiron Institute - Simons Foundation

DeepSEA analysisDeepSEA is a deep learning framework that predicts genomic variant effects on a wide range of regulatory features with single nucleotide sensitivity: transcription factors binding, DNase I hypersensitive sites, and histone marks in multiple human cell types.

Submit a DeepSEA analysis

DeepSEA analysis
DeepSEA is a deep learning framework that predicts genomic variant effects on a wide range of regulatory features with single nucleotide sensitivity: transcription factors binding, DNase I hypersensitive sites, and histone marks in multiple human cell types.