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Genomedata specifications

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Unique identifier OMICS_02148
Name Genomedata
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux, Mac OS
Programming languages C, Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.4.1
Stability Stable
Maintained Yes

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Publication for Genomedata

Genomedata citations

 (13)
library_books

Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation

2017
J Exp Bot
PMCID: 5429002
PMID: 28338822
DOI: 10.1093/jxb/erx010

[…] analysing the rna-seq data (deposited in ncbi sequence read archive (sra) database with bioproject id prjna354681). the reads were mapped on the pigeonpea genome (; http://www.icrisat.org/gt-bt/iipg/genomedata.zip) using a splice-aware alignment algorithm, tophat (v 2.1.0) (). thereafter, the mapped reads were assembled into transcripts and their abundances were estimated using cufflinks (v […]

library_books

The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression

2017
Sci Rep
PMCID: 5259786
PMID: 28117353
DOI: 10.1038/srep41061

[…] analysis of global expression changes and ontology network assessment on the 2445 differentially selected genes was performed using mathematica® v10. ontology groups were generated using inbuilt genomedata, matching the annotated genes with pre-defined processes and intracellular functions. ontological information for gene processes was found for 1660 genes matching 1446 processes. two […]

library_books

Genome wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini seq)

2016
Nucleic Acids Res
PMCID: 5137433
PMID: 27587586
DOI: 10.1093/nar/gkw760

[…] sequence tag enrichment was then detected using sicer (v1.1, http://www.ncbi.nlm.nih.gov/pubmed/19505939). in order to be able to process data aligned to grch37 with this algorithm the genomedata class had to be amended accordingly. the wrapper shell scripts have been amended, so that several instances of the program could be executed in parallel. sicer was then run […]

library_books

Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)

2015
Plant Biotechnol J
PMCID: 5054876
PMID: 26397045
DOI: 10.1111/pbi.12470

[…] incidence score from 0% to 100% for fw and 0% to 100% for smd., icpl 20096 short reads were aligned to the publicly available pigeonpea genome of asha (icpl 87119) (http://www.icrisat.org/gt-bt/iipg/genomedata.zip)., parents and bulks used for seq‐bsa analysis., parents and bulks used for nonsynonymous snp (nssnps) analysis., parents used for expression profiling studies., parents and bulks used […]

library_books

De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes

2015
PLoS One
PMCID: 4482647
PMID: 26114291
DOI: 10.1371/journal.pone.0129016

[…] mays) []., the following genomes were obtained from other sources: kiwifruit (actinidia chinensis) [], sugar beet (beta vulgaris) []; pigeonpea (cajanus cajan) [] http://www.icrisat.org/gt-bt/iipg/genomedata.zip; pepper (capsicum annuum) []; chickpea (cicer arietinum) [] http://www.icrisat.org/gt-bt/icggc/genomedata.zip; lotus japonicus [] ftp://ftp.kazusa.or.jp/pub/lotus/lotus_r2.5/; banana […]

library_books

Novel scripts for improved annotation and selection of variants from whole exome sequencing in cancer research

2015
PMCID: 4487347
PMID: 26150983
DOI: 10.1016/j.mex.2015.03.003

[…] meticulously, but can have great impact in narrowing the scope. in hematological malignancies this search array can be defined as following, where the phrases reflects entries in wolfram research genomedata:mutvepannosc = {“signaltransduction”, “celladhesion”, “signalingpathway”, “differentiation”, “cellproliferation”, “regulationoftranscription”, “blood”, “apoptosis”, “inflammatoryresponse”, […]


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Genomedata institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
Genomedata funding source(s)
Supported by National Institutes of Health (HG004695).

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