DeepSEA specifications

Information


Unique identifier OMICS_13506
Name DeepSEA
Interface Web user interface
Restrictions to use None
Input data DNA sequence, chromatin regions-hg19 coordinates, variants sequence
Input format FASTA, BED, VCF
Output format ZIP, tab-delimited file
Computer skills Basic
Stability Stable
Source code URL http://deepsea.princeton.edu/media/code/deepsea.v0.94.tar.gz
Maintained Yes

Documentation


Maintainer


  • person_outline Olga G. Troyanskaya <>

Information


Unique identifier OMICS_13506
Name DeepSEA
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data DNA sequence, chromatin regions-hg19 coordinates, variants sequence
Input format FASTA, BED, VCF
Output data DNA sequence feature predictions, variant effect predictions
Output format ZIP, tab-delimited file
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Olga G. Troyanskaya <>

Publication for DeepSEA

DeepSEA in publications

 (52)
PMCID: 5954283
PMID: 29764360
DOI: 10.1186/s12864-018-4459-6

[…] methods fail to exploit sequence information except speid. at the meantime, there are many inspiring methods for 1d chromatin states prediction [, ], including gkmsvm for enhancer prediction [], deepsea for epigenomic state prediction [] and deepbind for dna/rna-binding proteins prediction [], which extract sequence features and yield high performance. gkmsvm transforms variable-length […]

PMCID: 5904163
PMID: 29666371
DOI: 10.1038/s41467-018-03554-9

[…] (r2 = 0.98), showed a predicted increase in binding of ctcf, which is a tf known to mediate chromosomal interactions (fig. ).fig. 4, we also used the deep learning–based sequence analyzer (deepsea) to examine the allelic effect on protein binding of rs4776984 and the 15 other looping cis-eqtls of map2k5. of these 16 looping cis-eqtls, six were potentially functional and of these, two […]

PMCID: 5898002
PMID: 29650021
DOI: 10.1186/s12934-018-0908-9

[…] broad substrate promiscuity displayed by type iii pkss makes them wonderful candidates for expanding chemical diversity of polyketides., violapyrone b (vlp b, 10), an α-pyrone compound produced by deepsea-derived streptomyces somaliensis scsio zh66, is encoded by a type iii pks vioa. we overexpressed vioa in three different hosts, including streptomyces coelicolor m1146, streptomyces sanyensis […]

PMCID: 5938574
PMID: 29618526
DOI: 10.1098/rsif.2017.0387

[…] multi-task learning is an approach related to transfer learning. in a multi-task learning framework, a model learns a number of tasks simultaneously such that features are shared across them. deepsea [] implemented multi-task joint learning of diverse chromatin factors from raw dna sequence. this allowed a sequence feature that was effective in recognizing binding of a specific tf […]

PMCID: 5877348
PMID: 29553064
DOI: 10.1264/jsme2.ME17197

[…] were 73% (rmhr-r28hr1), 62% (rmhr-r28hr2), and 57% (r28hr1-r28hr2) respectively. no rhodopsin gene was found in the genome of r. profundi saoric-476t. although r28hr1 and r28hr2 were found from the deepsea isolate, it currently remains unclear whether these are deep-sea adapted rhodopsins because the habitat of the genus rubrivirga is not yet understood. in the blastp search […]


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DeepSEA institution(s)
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA; Department of Computer Science, Princeton University, Princeton, NJ, USA; Simons Center for Data Analysis, Simons Foundation, New York, NY, USA
DeepSEA funding source(s)
This work was primarily supported by US National Institutes of Health (NIH) grants R01 GM071966 and R01 HG005998; and in part by the US National Science Foundation (NSF) CAREER award (DBI-0546275), NIH award T32 HG003284 and NIH grant P50 GM071508 and by the Genetic Networks program of the Canadian Institute for Advanced Research (CIFAR).

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