New job

To run Sequence Profiler with the newest DeepSEA model, visit: https://hb.flatironinstitute.org/deepsea/?analysis=insilico

What is Sequence Profiler?

Sequence Profiler is a ultility of DeepSEA that performs "in silico saturated mutagenesis" analysis for discovering informative sequence features within any sequence. Specifically it performs computational mutation scanning and inspect effects of mutating every base of the input sequence on chromatin feature prediction. This method for context-specific sequence feature extraction fully utilizes the DeepSEA’s capability of utilizing flanking context sequences information.

Please enter the information to run a new Sequence Profiler Analysis.

Paste enter a 1000bp sequence or a genomic region or a variant and specify the type (if a variant is specified, 1000bp region centering at the variant will be used):

Content*

File type*

Chrom feat type*

Cell type*

Treatment*

Title

Email address you want the results sent to. (Optional)

FASTA format:

Each section starts with '>'.
The sequence has to have length of 1000bp.
Allowed nucleic acid codes: ATCGatcg (lowercases are treated the same of uppercases).

Example file: FASTA

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 file: BED

VCF format:

Each line has at least 5 tab separated fields.
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. Empty or contain one or more upper case codes from ATCG. Maximum 100 characters.

Example file: VCF