VecScreen statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

VecScreen specifications

Information


Unique identifier OMICS_18155
Name VecScreen
Interface Web user interface
Restrictions to use None
Input data A query sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


VecScreen citations

 (194)
library_books

Microscopic and Molecular Evidence of the First Elasmobranch Adomavirus, the Cause of Skin Disease in a Giant Guitarfish, Rhynchobatus djiddensis

2018
MBio
PMCID: 5954223
PMID: 29764943
DOI: 10.1128/mBio.00185-18

[…] sequencing reagents (Illumina MiSeq Reagents V2; 500 cycles).A total of 8,119.238 million reads were generated and analyzed as previously described (). Adaptor and primer sequences were trimmed using VecScreen, while duplicate reads and low-sequencing-quality tails were removed using a Phred quality score of 10 as the threshold. The cleaned reads were de novo assembled using an in-house sequence a […]

call_split

Elucidation and functional characterization of CsPSY and CsUGT promoters in Crocus sativus L.

2018
PLoS One
PMCID: 5892871
PMID: 29634744
DOI: 10.1371/journal.pone.0195348
call_split See protocol

[…] g TA cloning kit (Fermentas). Plasmids were isolated from different clones and were then processed for sequencing after purification. For removal of vector contamination, sequences were trimmed using VecScreen software (https://www.ncbi.nlm.nih.gov/tools/vecscreen/) and were aligned by BLASTn and ClustalW program. The presence of putative cis-regulatory elements were detected by PLACE (http://www. […]

library_books

Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes

2018
Virol J
PMCID: 5769433
PMID: 29334978
DOI: 10.1186/s12985-018-0923-9

[…] icates and only one random copy of duplicates was kept. Low sequencing quality tails were trimmed using Phred quality score ten as the threshold. Adaptors were trimmed using the default parameters of VecScreen which is NCBI BLASTn with specialized parameters designed for adapter removal. The cleaned reads were de-novo assembled within each barcode by SOAPdenovo2 version r240 using Kmer size 63 wit […]

call_split

The rumen microbiome: an underexplored resource for novel antimicrobial discovery

2017
PMCID: 5711939
PMID: 29214045
DOI: 10.1038/s41522-017-0042-1
call_split See protocol

[…] owing sequence assembly using the default parameters on the gsAssembler software v.2.5.3 (Roche Life Sciences), sequences were trimmed and vector sequence were removed using BioEdit (version 7.1.11). VecScreen on NCBI was used to search the sequences for vector contamination. ORFs were determined using NCBI’s ORF finder on the NCBI blast suite (v2.2.28). […]

call_split

Exploration for the Salinity Tolerance Related Genes from Xero Halophyte Atriplex canescens Exploiting Yeast Functional Screening System

2017
Int J Mol Sci
PMCID: 5713411
PMID: 29149055
DOI: 10.3390/ijms18112444
call_split See protocol

[…] erance was performed at Beijing Genomic Institute, China, with primer pair T7 and pYES-R (). After sequencing, vector sequences were trimmed using SeqMan II (DNASTAR, Inc., Madison, WI, USA) and NCBI VecScreen (http://www.ncbi.nlm.nih.gov/tools/vecscreen/). Trimmed cDNA sequences were assembled using Vector NTI (Invitrogen, Carlsbad, CA, USA). Contigs were built using the CAP3 assembly program [] […]

library_books

Structure, target specificity and expression of PN_LNC_N13, a long non coding RNA differentially expressed in apomictic and sexual Paspalum notatum

2017
Plant Mol Biol
PMCID: 5778186
PMID: 29119346
DOI: 10.1007/s11103-017-0679-4

[…] Vector contaminations were identified and removed by using the VecScreen tool at the National Center for Biotechnology Information (NCBI) webpage (http://www.ncbi.nlm.nih.gov/VecScreen/). Aligments were done with Clustal Omega on the EBI-EMBL website (http://www. […]

Citations

Looking to check out a full list of citations?

VecScreen reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review VecScreen