---
title: DeepSol inputs and parameters
description: >-
  Protein sequence requirements and parameters for DeepSol solubility
  prediction.
---

You provide a protein as an amino acid sequence — pasted directly, fetched from a UniProt accession, or uploaded in FASTA. The one thing that most affects your result is submitting the true expressed construct: use standard residues only, and match the mature sequence (signal peptides removed, tags included) to the protein you actually plan to express.

## Supported inputs

DeepSol accepts protein sequences for E. coli expression solubility prediction. The CNN architecture exploits k-mer structure and combines sequence-level features with structural properties from SCRATCH-1D predictions.

## Webapp input methods

The .bloom* webapp provides two input modes:

### Sequence input (default)
- **Protein Sequence**: Paste the amino acid sequence in single-letter code directly
- **Format**: Raw sequence without FASTA header
- **Example**: `MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR`

### UniProt Accession input
- **Accession ID**: Enter a valid UniProt accession (e.g., P68871)
- **Auto-fetch**: The system automatically retrieves the protein sequence from UniProt
- **Validation**: Real-time checking of accession format

## File-based inputs

- **FASTA files (preferred):** standard FASTA format with header lines starting with `>`; UTF-8 encoded.
- **Raw sequences:** single amino acid sequences in one-letter code; one sequence per line.
- **Batch CSV:** header `sequence`; optional `id` column is echoed back in results.

## Sequence requirements

- **Amino acids:** Standard 20 amino acids only (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y).
- **Sequence length:** Recommended range 50-2000 residues; very short or very long sequences may have reduced accuracy.
- **No ambiguous residues:** Avoid X, B, Z, J, or other non-standard characters.
- **Single chain:** Submit one polypeptide chain per entry; multi-chain complexes should be split.

## Webapp parameters

The following options are available in the .bloom* webapp interface:

### SCRATCH-1D features
- **Use SCRATCH-1D** (toggle, default: enabled)
- Enables additional structural feature extraction using SCRATCH-1D predictions

### Model selection
- **Model**: Choose between `deepsol1`, `deepsol2`, or `deepsol3`
- Each version has different training data and performance characteristics

### Processing mode
- **Mode**: Select the operation type
  - `preprocess` - Data preprocessing only
  - `train` - Model training (advanced)
  - `decode` - Generate predictions
  - `cv` - Cross-validation mode

### Pipeline stage
- **Stage**: Select processing stage (1 or 2)

### Compute device
- **Device**: Choose between `cpu` or `cuda` (GPU acceleration)

### Advanced options (optional)
- **Config File Path**: Path to custom DeepSol configuration
- **Keras Backend**: Specify Keras backend (tensorflow, theano, cntk)
- **CUDA Root Path**: Root path for CUDA installation if using GPU
- **Test File Name**: Name of test data file for evaluation

## Validation rules

- Sequences containing non-standard amino acids will be rejected.
- Sequences shorter than 10 residues may produce unreliable predictions.
- Very long sequences (>3000 residues) may timeout; consider domain-based splitting.
- Numerical characters, spaces, and special symbols are stripped automatically.

## Preparing data

- Remove signal peptides and pro-domains if predicting mature protein solubility.
- Ensure sequences represent the actual expressed construct (include tags if used).
- For fusion proteins, submit the complete fusion sequence.
- Remove any formatting characters (line breaks within sequences, numbering).

## Submission tips

- Keep batches under ~1,000 sequences for faster feedback; large collections should be chunked.
- Retry on `429` with exponential backoff; respect workspace rate limits.
- Store original input order externally; outputs are returned in processed order.
- Include descriptive FASTA headers to track sequences through the pipeline.

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