NCBI Genome Workbench statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

NCBI Genome Workbench specifications

Information


Unique identifier OMICS_00920
Name NCBI Genome Workbench
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 2.12.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


NCBI Genome Workbench citations

 (7)
call_split

Whole genome sequencing reveals a 7 base pair deletion in DMD exon 42 in a dog with muscular dystrophy

2016
Mamm Genome
PMCID: 5371640
PMID: 28028563
DOI: 10.1007/s00335-016-9675-2
call_split See protocol

[…] e from genotype and probability of the called genotype. Mapping quality was performed by Phred-scaled probability of all samples and reported in −log. National Center for Biotechnology Information’s (NCBI) Genome Workbench software (Bethesda, MD) was used to evaluate mutations, SNPs, and indels within the DMD gene (compared to the CanFam3.1 whole genome shotgun sequence used as the reference) (Hoe […]

library_books

Prediction of Host Derived miRNAs with the Potential to Target PVY in Potato Plants

2016
Front Genet
PMCID: 5022016
PMID: 27683585
DOI: 10.3389/fgene.2016.00159

[…] gous sequences were retrieved and aligned using the Muscle alignment tool (Edgar, ) along with the query sequence. Aligned sequences were used to build a phylogenetic tree using a poison algorithm by NCBI Genome Workbench. […]

library_books

A Family of CSαβ Defensins and Defensin Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis

2016
PLoS One
PMCID: 4996505
PMID: 27556587
DOI: 10.1371/journal.pone.0161585

[…] from various body parts [] for any defensin precursors using various defensin sequences (marked in bold in ); (ii) We used a collection of insect defensin sequences () to generate a BLAST database in NCBI Genome Workbench 2.8.10 (available at http://www.ncbi.nlm.nih.gov/tools/gbench/), and carried out tblastx queries with a cut-off of 10−5 against our database using L. migratoria palpi transcripto […]

library_books

Comparative analysis of plastid genomes of non photosynthetic Ericaceae and their photosynthetic relatives

2016
Sci Rep
PMCID: 4958920
PMID: 27452401
DOI: 10.1038/srep30042

[…] rrespective of the e-value. Circos was then used to generate diagrams of the repeats. The same set of parameters was used to calculate repeats for . For dot plot diagrams (), BLASTN self-alignment in NCBI Genome Workbench 2.9.5 ( http://www.ncbi.nlm.nih.gov/tools/gbench/ was performed with a word size of 9 bp and a maximum e-value of 10−5. The low-complexity filter (“-dust no” option) was switched […]

call_split

Draft Genome Sequence of Bacillus atrophaeus UCMB 5137, a Plant Growth Promoting Rhizobacterium

2013
Genome Announc
PMCID: 3707584
PMID: 23788535
DOI: 10.1128/genomeA.00233-13
call_split See protocol

[…] 3 and CLC Genomics Workbench 5. The draft assembled contigs were aligned against the complete reference genome sequence of B. atrophaeus 1942 using the r2cat program () and the NG Aligner tool of the NCBI Genome Workbench v.2.5.5. The overlapping fragments were merged into larger contigs. Open reading frame (ORF) prediction and functional annotation of the predicted genes were done by GeneMark.hmm […]

library_books

Diversity and evolution of multiple orc/cdc6 adjacent replication origins in haloarchaea

2012
BMC Genomics
PMCID: 3528665
PMID: 22978470
DOI: 10.1186/1471-2164-13-478

[…] s. The GC plot was drawn using DNAplotter (window size: 50000; step size: 1000) []. Genome context analysis of the regions flanking the orc/cdc6-associated replication origins was performed using the NCBI Genome Workbench and scrutinized manually. Gene analysis was carried out using BlastP against the NCBI non-redundant proteins database ( http://blast.ncbi.nlm.nih.gov/). […]

Citations

Looking to check out a full list of citations?

NCBI Genome Workbench reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review NCBI Genome Workbench