What is the difference between a Strong and a Weak match?

They are NCBI VecScreen categories, set by the raw alignment score and by where the match sits. A terminal match — one reaching within 25 bases of an end — is believed on less evidence than one in the middle, so the two have different thresholds. Strong is very likely real contamination; Weak may be chance.

Why did a clean insert match a vector record?

Some genuine biological sequence is also in UniVec, because it is used as a vector element — yeast ADH1 promoter and selection markers are common examples. The matched record is named and linked, so a match can be checked rather than assumed to be contamination.

Does a clean screen mean my sequence is definitely vector-free?

It means nothing in it matches UniVec above the reporting floor. UniVec is broad but finite, so a clean screen is evidence of absence only for the vectors, adapters, linkers and primers it covers.

Sequencing

Screen for vector contamination

Find sequence that came from the vector rather than from the insert. A construct, a selected region or a set of reads is screened against NCBI UniVec — the reference database of vectors, adapters, linkers and primers — and every match is reported with the category NCBI assigns it, drawn on the map, and offered back masked or trimmed.

Open Screen for vector contamination Open the Vector contamination screen sample

One yeast locus with a KanMX4 cassette knocked in and the same locus without it — a real internal contaminant and its control

What it does

01Screen a construct, a selected region, pasted sequence or a set of reads against NCBI UniVec
02NCBI VecScreen's Strong / Moderate / Weak categories, with terminal and internal matches judged separately
03Suspect-origin segments: short stretches stranded between two vector matches
04Every match drawn on the plasmid map, with its score, strand and matched UniVec record
05Masked FASTA and trimmed-insert download
06Both UniVec builds — the curated core set and the full set
07Every search parameter and category threshold adjustable, defaulting to NCBI values

What it runs on

Reproduces NCBI VecScreen. The search is validated against the real NCBI BLAST+ blastn under VecScreen's published parameters, and the low-complexity masking against the reference symmetric-DUST implementation, over the whole bundled UniVec build. The panel runs on @ports/vecscreen.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

What is the difference between a Strong and a Weak match?: They are NCBI VecScreen categories, set by the raw alignment score and by where the match sits. A terminal match — one reaching within 25 bases of an end — is believed on less evidence than one in the middle, so the two have different thresholds. Strong is very likely real contamination; Weak may be chance.
Why did a clean insert match a vector record?: Some genuine biological sequence is also in UniVec, because it is used as a vector element — yeast ADH1 promoter and selection markers are common examples. The matched record is named and linked, so a match can be checked rather than assumed to be contamination.
Does a clean screen mean my sequence is definitely vector-free?: It means nothing in it matches UniVec above the reporting floor. UniVec is broad but finite, so a clean screen is evidence of absence only for the vectors, adapters, linkers and primers it covers.

Also searched as

vector contamination screen · vecscreen online · univec search · find vector sequence in my read · trim vector from sequence · adapter contamination check · remove cloning vector before submission · genbank submission vector screen · is there plasmid backbone in my insert · screen sanger read for vector · detect linker and primer contamination