NCBI Genome Workbench protocols

View NCBI Genome Workbench computational protocol

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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

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Documentation


NCBI Genome Workbench in pipeline

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

[…] 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/)., the authors declare […]


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NCBI Genome Workbench in publications

 (12)
PMCID: 5753643
PMID: 29194349
DOI: 10.3390/vetsci4040063

[…] x62477 (felis catus gene for fel d 1 protein chain 1) and x62478 (felis catus gene for fel d 1 protein chain 2). the graphic representation of the mutation points identified was realized in ncbi genome workbench tool., the amplifications provided fragments of approximately 1700 bp and 2500 bp from ch1 and ch2, respectively., for ch1, sequencing data from one siberian and one […]

PMCID: 5347006
PMID: 28287142
DOI: 10.1038/srep44084

[…] sequencing (ngs) laboratory and analysis workflow has been reported and data uploaded (genbank accessions kx574861-kx574908 inclusive). bam illumina sequence files were assembled and visualized with ncbi genome workbench and integrative genomics viewer. supporting information methods contains primers for pcr amplification and dideoxy sequencing of selected regions of hsv-2 dna (), rapid […]

PMCID: 5217101
PMID: 27852011
DOI: 10.1534/g3.116.035923

[…] sequences, and significant hits were manually verified by synteny analysis and/or reciprocal best blastn searches of nucleotide databases, using segments of the chicken genome as queries., the ncbi genome workbench tool (version 2.10.0) was used to compare the alignments between an assembled region of the chicken major histocompatibility complex (mhc) from bird #256 (accession no. […]

PMCID: 5022016
PMID: 27683585
DOI: 10.3389/fgene.2016.00159

[…] 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., different families of mirnas of solanum tuberosum have considerable potential to target potato virus-y. mirna families, such as mir166c-3p, mir482e-5p, mir5303a, mir5303d, […]

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

[…] 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 […]


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