> This page is for MSA Search, version 2.6.0 (Latest) (default).
> For other versions, use one of these documentation indexes:
> - 2.6.0 (Latest) (default): https://docs.nvidia.com/nim/bionemo/msa-search/2.6.0/llms.txt
> - 2.5.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.5.0/llms.txt
> - 2.4.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.4.0/llms.txt
> - 2.3.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.3.0/llms.txt
> - 2.2.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.2.0/llms.txt
> - 2.1.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.1.0/llms.txt
> - 2.0.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.0.0/llms.txt
> - 1.0.0: https://docs.nvidia.com/nim/bionemo/msa-search/1.0.0/llms.txt

> For clean Markdown of any page, append .md to the page URL.
> For a complete documentation index, see https://docs.nvidia.com/nim/bionemo/llms.txt.
> For AI client integration (Claude Code, Cursor, etc.), connect to the MCP server at https://docs.nvidia.com/nim/bionemo/_mcp/server.

## Release 2.6.0

### Summary

This release introduces experimental batch search and file output capabilities, enabling high-throughput MSA generation workflows. It also raises the maximum input sequence length from 4,096 to 10,240 characters.

### New Features

#### Batch Search API (Experimental)

All three search endpoints now accept batch inputs when the NIM is started with `NIM_EXPERIMENTAL=1`:

* **Monomer and template search**: Pass `sequence` as a list of strings instead of a single string
* **Paired search**: Pass `sequences` as a list of lists (each inner list is one complex)
* **Per-item status**: The response wraps individual results in a `results` array; failed items do not affect other items in the batch
* **Configurable limit**: Maximum batch size is controlled by `NIM_MSA_API_MAX_BATCH_SIZE` (default: 300)

Refer to [Batch Search (Experimental)](/nim/bionemo/msa-search/batch-search-experimental) for endpoint details and examples.

#### File Output Mode (Experimental)

When `NIM_EXPERIMENTAL=1` and `NIM_MSA_OUTPUT_DIRECTORY` are set, the NIM writes alignment files to disk for batch requests and returns `file://` URI references instead of inline content. Non-batch responses remain inline. Files are written to a temporary location and then renamed into place using POSIX `rename()`. On filesystems that provide atomic rename semantics (local disk, NFS), readers do not observe partial content; verify that your storage backend supports POSIX rename semantics if atomicity is required.

Refer to [File Output Mode](/nim/bionemo/msa-search/batch-search-experimental#file-output-mode-optional) for configuration details.

#### Increased Maximum Sequence Length

The maximum input protein sequence length is raised from 4,096 to 10,240 characters. This applies to all search endpoints and is controlled by `NIM_MSA_API_MAX_SEQUENCE_LENGTH` (default: `10240`).

### Migration Notes

No breaking changes. All experimental features are opt-in and require `NIM_EXPERIMENTAL=1`. The increased sequence-length limit is backward compatible.