Add Dayhoff FASTA and MMseqs2 databases

README.md

@@ -1,3 +1,117 @@
 ---
-license: mit
+pretty_name: Dayhoff FASTA and MMseqs2 Databases
 ---
+
+# Dayhoff FASTA and MMseqs2 databases
+
+This dataset contains the original [Dayhoff Atlas](https://huggingface.co/datasets/microsoft/Dayhoff) GigaRef and UniRef50 datasets, in formats amenable to MMSeqs2 CPU and GPU utilities.
+
+The train, validation, and test sets from the original atlas were combined and the following datasets available:
+
+* GigaRef No Singletons - The GigaRef dataset, with no singleton clusters.
+* GigaRef Singletons - The GigaRef dataset, with only singleton clusters.
+* GigaRef Full - Every sequence contained in both the no-singletons and singletons subsets.
+* UniRef50 - UniProt clustered at 50% sequence identity.
+
+Each dataset is or will be available in the following formats:
+
+* FASTA - Canonical sequence storage format, usable with many bioinformatics tools.
+* MMSeqs2-CPU - Converted folder of unindexed database files compatible with MMSeqs2-CPU. Searches can be tuned to splits that accommodate your system RAM.
+* MMSeqs2-GPU - Converted folder of padded sequence databases for MMSeqs2-GPU search. Requires 1+ GPU(s) on your machine to run.
+
+## Current Repo Organization
+
+```text
+fastas/
+├── gigaref-full.fasta.gz
+├── gigaref-singletons.fasta.gz
+├── gigaref-no-singletons.fasta.gz
+└── uniref50.fasta.gz
+
+mmseqs-cpu/
+└── gigaref-no-singletons/db/
+
+mmseqs-gpu/
+└── gigaref-no-singletons/db_gpu/
+```
+
+MMseqs can read the `.fasta.gz` files directly.
+
+| Artifact | Download | Working disk | Host RAM | GPU |
+| --- | ---: | ---: | --- | --- |
+| GigaRef full FASTA | 358.90 GB | 358.90 GB compressed | Not applicable | None |
+| GigaRef singleton FASTA | 147.28 GB | 147.28 GB compressed | Not applicable | None |
+| GigaRef no-singleton FASTA | 211.62 GB | 211.62 GB compressed | Not applicable | None |
+| UniRef50 FASTA | 13.27 GB | 13.27 GB compressed | Not applicable | None |
+| GigaRef no-singleton CPU MMseqs | 279.08 GB | 572.73 GB extracted; allow 647 GB while extracting | 64 GB is a practical starting point with splitting; 600+ GB maximizes  throughput | None |
+| GigaRef no-singleton GPU MMseqs | 292.13 GB | 586.94 GB extracted; allow 660 GB while extracting | 64 GB is a practical starting point with splitting; 600+ GB maximizes throughput | At least one MMseqs2-GPU-compatible NVIDIA GPU; the database need not fit VRAM |
+
+Put the extracted MMseqs database and temporary search directory on the
+fastest local SSD or NVMe available. I/O speed, RAM, and GPUs improve throughput;
+slow storage substantially increases search time.
+
+## Hugging Face download example
+
+```bash
+export REPO=microsoft/Dayhoff-MMseqs2
+export REV=main
+export DEST=/data/Dayhoff-MMseqs2
+export TARGET=gigaref-no-singletons
+
+# FASTA
+hf download "$REPO" "fastas/$TARGET.fasta.gz" \
+  --repo-type dataset --revision "$REV" --local-dir "$DEST"
+
+# CPU MMseqs
+hf download "$REPO" --repo-type dataset --revision "$REV" \
+  --include "mmseqs-cpu/$TARGET/**" --local-dir "$DEST"
+
+# GPU MMseqs
+hf download "$REPO" --repo-type dataset --revision "$REV" \
+  --include "mmseqs-gpu/$TARGET/**" --local-dir "$DEST"
+```
+
+Valid FASTA targets are `gigaref-full`, `gigaref-singletons`,
+`gigaref-no-singletons`, and `uniref50`. Only
+`gigaref-no-singletons` currently has CPU and GPU MMseqs databases.
+
+## Extract and search
+
+The FASTA needs no extraction for MMseqs. To create an uncompressed FASTA:
+
+```bash
+pigz -dc "fastas/$TARGET.fasta.gz" > "fastas/$TARGET.fasta"
+```
+
+Extract either MMseqs representation once:
+
+```bash
+find "mmseqs-cpu/$TARGET" -type f -name '*.gz' -print0 |
+  xargs -0 -n1 pigz -d
+
+find "mmseqs-gpu/$TARGET" -type f -name '*.gz' -print0 |
+  xargs -0 -n1 pigz -d
+```
+
+The resulting target prefixes are:
+
+```text
+mmseqs-cpu/gigaref-no-singletons/db/db
+mmseqs-gpu/gigaref-no-singletons/db_gpu/db_gpu
+```
+
+For a 64 GB host, use native MMseqs target splitting:
+
+```bash
+mmseqs search queryDB TARGET_DB resultDB tmp \
+  --gpu 1 \
+  --split-mode 0 \
+  --split-memory-limit 48G \
+```
+
+Omit `--gpu 1` for CPU search.
+
+The no-singletons FASTA and MMseqs database contain the same
+1.8B-sequence corpus. The FASTA uses 
+`gr_<source-index>` identifiers, while the existing MMseqs database retains
+older `g<part>_<row>` identifiers. We are patching this in a future update but it should have no effect on inference.

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