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SDhaP specifications

Information


Unique identifier OMICS_08167
Name SDhaP
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Shreepriya Das <>

Publication for SDhaP

SDhaP in publications

 (22)
PMCID: 5954289
PMID: 29764364
DOI: 10.1186/s12864-018-4464-9

[…] [] relied on a graphical approach to develop a scheme which resolves conflicts arising from incorrect haplotype phasing. haptree [] investigated the polyploid setup using a branch-and-bound scheme. sdhap [] formulates the haplotype assembly problem as a semi-definite program and exploits its special structure, the low rank of the underlying solution, to solve it rapidly and with high accuracy. […]

PMCID: 5915555
PMID: 29720992
DOI: 10.3389/fpls.2018.00513

[…] sequence reads (figure )., a number of different polyploid haplotyping tools (for sequence reads) have been developed in recent years, including polyhap (), satlotyper (), hapcompass (), haptree (), sdhap (), shesisplus (), and tripoly (motazedi et al., unpublished). three of these tools (hapcompass, haptree, and sdhap) were recently compared and evaluated over a range of different simulated […]

PMCID: 5846771
PMID: 29529047
DOI: 10.1371/journal.pone.0193928

[…] 9 and linked primarily repetitive sequences to annotated genes of unknown function such as ak308561 or ak131020. also on chromosome 5 we found a recurrent link between sdha and the pseudogene sdhap3. both types of events are likely artifacts due to misalignment not filtered out due to differences in the breakpoint coordinates., exact breakpoint recurrence cannot be used as a parameter […]

PMCID: 5836820
PMID: 29504908
DOI: 10.1186/s12920-018-0327-0

[…] sdha, sdhb, sdhc, sdhd, nf1, ret, hras, kras, epas1 (hif2a), atrx, csde1, braf, fgfr1, fgfr2, fgfr3, fgfr4, fgfrl1, setd2, arnt, tp53, tp53bp1, tp53bp2, tp53i13, kmt2d, bap1, idh1, idh2, sdhaf1, sdhap2, fh, egln1, mdh2, tmem127, max, kif1b, men1, gdnf, gnas, cdkn2a, brca1, and brca2. selected genes are involved in many important pathways including tca cycle, dna repair, oxidative […]

PMCID: 5698427
PMID: 29162797
DOI: 10.1038/s41467-017-01556-7

[…] (http://www.cbioportal.org/study?id=brca_metabric). we were able to map 59 out of 70 cinp genes to metabric microarray data (missing genes: znf532, trmt13, amigo2, kin, nkx3-1, tanc2, tvp23c, sdhap1, mtnd2p28, gtf2ip4, h2bfs). survival analysis was performed using the same method as described above for tcga data. the cox multiple regression uses cinp score, age, and three molecular […]


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SDhaP institution(s)
Department of ECE, The University of Texas at Austin, Austin, Austin, USA

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