Vectors
Vector feature annotator
Automatically detect promoters, tags, protease sites and recombination sites in a vector sequence, add your own features, and export an annotated GenBank file.
Detected features
Nothing from the library matched. Raise the mismatch allowance, or add your own feature in the section below.
Add your own feature
The built-in library holds only short, well-established motifs. For long features such as the CMV promoter, a resistance gene or an origin of replication, copy the sequence from your own map and add it here; it stays in your browser for this session.
Tags and protease sites are searched at the protein level: all six reading frames are translated and the motif is sought in each. That finds a tag whatever codons were used, but it also means a chance match can appear in the wrong frame — the evidence column shows the frame so you can judge. The mismatch allowance applies to DNA patterns only.
Formula
motif → six-frame translation → DNA coordinates
- DNA pattern
- searched on both strands, with IUPAC ambiguity codes understood
- protein motif
- all six frames are translated and the motif is sought in each
- mismatch allowance
- applies to DNA patterns only, never to protein motifs
Worked example
Why a His tag escapes a DNA search but not a protein search
- first construct: CACCACCACCACCACCAC
- second construct: CATCATCATCATCATCAT
- third construct: CACCATCACCATCACCAT
- All three DNA sequences are completely different, so one DNA pattern finds at most one of them.
- But all three translate to HHHHHH.
- The tool translates the sequence in six frames and looks for HHHHHH in the translations.
- It then maps the amino acid position back to DNA coordinates.
Answer all three are found by a single motif, whatever codons the designer chose
Common mistakes
- Trusting protein matches without reading the evidence column. Searching six frames means a short motif can turn up by chance in the wrong frame; the frame is printed so you can judge.
- Expecting the CMV promoter or a resistance gene to be found. The built-in library holds only short, well-established motifs; features hundreds of bases long must be copied from your own map and added below.
- Raising the mismatch allowance without reason. At two mismatches on an eighteen-base motif, chance hits multiply quickly.
- Unticking the option that keeps existing features. With it off, the original annotation of your GenBank file is dropped from the output and only the automatic hits remain.
Frequently asked
Is a custom feature I add saved?
No — it lives in your browser for this session only. To make it permanent, add a row to the feature_library table.
Why does one motif appear twice in the list?
Because it matched on both strands, or in more than one frame. The strand and evidence columns show the difference; untick the ones you do not want.
Why is DDDDK found inside the FLAG tag?
Because the enterokinase site is DDDDK and the end of the FLAG sequence, DYKDDDDK, contains exactly that. The match is real rather than an error; which one to keep is your call.