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Protocols

UniVec specifications

Information


Unique identifier OMICS_14937
Name UniVec
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Univec

Maintainer


  • person_outline GeneMap Team

UniVec citations

 (162)
library_books

Evaluation of commercially available small RNASeq library preparation kits using low input RNA

2018
BMC Genomics
PMCID: 5936030
PMID: 29728066
DOI: 10.1186/s12864-018-4726-6

[…] rimmed as well.Reads that arise from human rRNA and contamination from library preparation protocols are removed before they are mapped to the human genome. The reads are first mapped to a library of UniVec contaminants, a collection of common vector, adapter, linker and PCR primer sequences collated by the NCBI. They are then mapped to human rRNA sequences obtained from NCBI The reads are mapped […]

call_split

The Effect of Hydrostatic Pressure on Enrichments of Hydrocarbon Degrading Microbes From the Gulf of Mexico Following the Deepwater Horizon Oil Spill

2018
Front Microbiol
PMCID: 5932198
PMID: 29755436
DOI: 10.3389/fmicb.2018.00808
call_split See protocol

[…] ality control and trimming of the bacterial and archaeal 16S rRNA sequences was performed with Geneious Pro software (v4.8.5; Biomatters Limited, Auckland, New Zealand) using the option ScreenVector (UniVec High Sensitivity, Min BLAST alignment score 20), an error probability limit of 0.05, and a minimum post-trimming read-length of 400 bp. Further analysis of the quality-filtered sequences was pe […]

call_split

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

2018
BMC Genomics
PMCID: 5902842
PMID: 29661190
DOI: 10.1186/s12864-018-4656-3
call_split See protocol

[…] nnecticut, USA) with settings “-m –large –het –cpu 32”. Also included in the Newbler assembly were 1,209,245 paired end sequences from a 4-kb insert library sequenced using 454 GS-FLX pyrosequencing. UniVec_Core (ftp://ftp.ncbi.nlm.nih.gov/pub/UniVec/UniVec_Core) and common sequencing primers were used for vector trimming during Newbler assembly, while the sequence of Escherichia coli DH10B (NC_01 […]

library_books

Phylogeny and putative virulence gene analysis of Bartonella bovis

2017
PMCID: 5938196
PMID: 29311425
DOI: 10.1292/jvms.17-0448

[…] cing data with highly uneven depth []. Only contigs larger than 200bp were used for downstream analysis. The assembled contigs were subjected to left over adapters and contaminant filter against NCBI univec database via seq clean (default parameter) (http://hpc.ilri.cgiar.org/seqclean/seqclean). The whole genome sequencing project has been submitted to the GenBank database (accession no: MWVG00000 […]

call_split

Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

2017
BMC Res Notes
PMCID: 5725652
PMID: 29228974
DOI: 10.1186/s13104-017-3018-6
call_split See protocol

[…] gments smaller than 200 bp. Back-mapping of input sequencing reads to the assembly using Salmon software, allowed removal of 4526 uncovered isoforms []. Finally, scanning the new assembly against the UniVec Database containing vector and artificial sequences eliminated 23 transcripts and trimmed an additional 98 transcripts []. In total, all filtration steps excluded 5332 transcripts. The final as […]

call_split

Impact of hormonal modulation at proestrus on ovarian responses and uterine gene expression of suckled anestrous beef cows

2017
PMCID: 5664832
PMID: 29118976
DOI: 10.1186/s40104-017-0211-3
call_split See protocol

[…] adaptors and low quality using SeqyClean v1.3.12. (https://github.com/ibest/seqyclean) using 26 Phred quality parameter for maximum average error and a fasta file with contaminant sequences from the Univec database (https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/). Only high quality paired-end sequences were kept for further analyses The reads were mapped with Bowtie2 v2.1.0 [] on the masked […]

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