GeneLoop documentation

What GeneLoop is

You keep your plasmids, notes, protocols and experiments in one project. You open a sequence and get the maps and analysis tools you would expect — plasmid map, linear map, digests, primers, restriction sites, alignments. Alongside them sits an assistant that can read your construct and help you design the next one.

The part worth understanding before anything else: the assistant never changes a sequence without leaving you something to check. Every edit produces a diff against the previous version, a list of the features it touched, and a saved revision you can go back to. It is closer to a colleague handing you a marked-up map than to a black box returning a finished plasmid.

Who it is for

People who clone. If you spend your week picking cut sites, checking reading frames, chasing a construct that will not express, or writing up what you did last Tuesday, this is built for your bench.

You do not need to write code. Everything in this documentation describes buttons, panels and plain-English requests. There is a programmatic interface if you want to script against the analysis tools, but it is entirely optional.

Before you start

You need three things, and you probably already have all of them.

• An account. Sign up at gene-loop.com. You can look around as a guest, but a guest cannot save, edit or export.
• A starting sequence. A GenBank or FASTA file, an Addgene or iGEM accession, or nothing at all — GeneLoop ships common backbones including pUC19, pET-28a(+), pcDNA3.1(+), pGEX-4T-1 and lentiCRISPR v2.
• A goal you can say out loud. “Put a His-tagged version of this gene into pET-28a so I can purify it from E. coli” is enough to start.

Your first construct

The shape of the work is the same whether you are moving one insert or building a five-part assembly.

1. 1

   Make a project

   A project holds everything for one piece of work — sequences, documents, protocols, experiments and the conversations about them. Most people use one per construct family or per aim. More on projects.
2. 2

   Bring in your backbone

   Import a file, paste a sequence, pick a stock vector, or ask the assistant to fetch a deposit by accession. GeneLoop keeps the annotations that came with it. More on importing.
3. 3

   Say what you want to build

   Open the chat and describe the construct in your own words. Name the host, the tag, the selection marker and the enzymes you have — the more of your actual constraints it knows, the less it has to assume. How to ask well.
4. 4

   Read the plan before it builds

   For anything more than a small edit, work in Plan mode first. The assistant cannot touch your files in Plan mode; it gathers evidence and writes a plan you approve or send back. Plan and Act.
5. 5

   Check the change, not the summary

   When a sequence changes, open the diff. Look at what moved, which features were cut or shifted, and whether the reading frame still starts where you think it does. Reviewing a change.
6. 6

   Verify, then export

   Run a verification pass and read the verdict before you spend money on DNA. Then export GenBank for your vendor or your next tool. Verification · Exporting.

The one habit worth forming

Read the sequence, not the sentence. The assistant writes fluent, confident prose, and fluent prose is not evidence. When it tells you a construct is in frame, the thing that makes that true is the diff, the translation and the verification verdict — all of which are one click away.

Everything in these docs is arranged around making that check cheap enough that you actually do it.

Where to go next

Getting help

If something is broken or behaving oddly, start with Troubleshooting — it covers the problems people actually hit. Otherwise write to support@gene-loop.com or use the contact form, and include the project name and roughly when it happened.