AtSubP 2.0

AtSubP-2.0 handbook

From sequence to localization

A concise guide to preparing Arabidopsis protein inputs, choosing prediction levels, running the model, and exporting results.

No account required

The web server is free to use. For questions, contact naveen.duhan@usu.edu.

1

Provide sequences

Enter NCBI or UniProt accessions, upload a file, or paste FASTA.

2

Choose levels

Select one or more prediction levels and a model strategy.

3

Review output

The completed run opens directly in the Results workspace.

01 · Input data

Three ways to provide proteins

Accessions

Enter multiple NCBI or UniProt protein accessions separated by commas or new lines. Fetch & preview is optional; Run Prediction can fetch them automatically.

Upload

Upload FASTA directly, or upload a TXT, CSV, or TSV accession list. Accession lists are fetched automatically.

Paste FASTA

Paste one or more amino-acid sequences. Every record must begin with a FASTA header using the > character.

Only amino-acid sequences are supported; nucleotide sequences should not be submitted.

02 · Model strategy

Choose speed or sensitivity

Fast

Uses dipeptide composition features. Best for larger protein sets and faster turnaround.

Sensitive

Uses tripeptide composition features. Best for smaller sets when prediction sensitivity is the priority.

03 · Prediction levels

A four-level hierarchy

Level I

Single vs dual

Determines whether a protein has one predicted localization or a dual localization.

Level II

Single localization

Classifies single-localized proteins into 12 cellular compartments.

Level III

Dual localization

Classifies dual-localized proteins into 9 supported compartment pairs.

Level IV

Membrane topology

Classifies predicted membrane proteins as single-pass or multi-pass.

04 · Run analysis

One primary action

Select the required levels and model, then choose Run Prediction. Processing status remains on the Prediction page; when the job finishes, the browser moves directly to Results. Email notification is optional.

05 · Read results

Save and navigate results

Copy the private results link when the job is submitted; it can reopen and monitor the job, and remains valid for 30 days. Completed outputs are organized from Level I through Level IV above a full-width, horizontally scrollable table. Download one level or export all available levels together.

06 · Compatibility

Supported browsers

OSVersionChromeFirefoxSafariEdge
LinuxUbuntu 22.04Chrome 108+Firefox 112+—Edge 113+
macOSVentura or laterLatestLatestSafari 16.4+Latest
Windows10 or 11Chrome 108+Firefox 112+—Edge 113+