Document UniRef50 and singleton MMseqs2 databases

README.md

@@ -29,10 +29,14 @@ fastas/
 └── uniref50.fasta.gz
 
 mmseqs-cpu/
-└── gigaref-no-singletons/db/
+├── gigaref-singletons/db/
+├── gigaref-no-singletons/db/
+└── uniref50/db/
 
 mmseqs-gpu/
-└── gigaref-no-singletons/db_gpu/
+├── gigaref-singletons/db_gpu/
+├── gigaref-no-singletons/db_gpu/
+└── uniref50/db_gpu/
 ```
 
 MMseqs can read the `.fasta.gz` files directly.
@@ -43,6 +47,10 @@ MMseqs can read the `.fasta.gz` files directly.
 | 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 |
+| UniRef50 CPU MMseqs | 14.97 GB | approximately 28 GB extracted | 32 GB recommended; lower RAM works with splitting | None |
+| UniRef50 GPU MMseqs | 15.29 GB | approximately 28 GB extracted | 32 GB recommended; lower RAM works with splitting | At least one MMseqs2-GPU-compatible NVIDIA GPU |
+| GigaRef singleton CPU MMseqs | 182.49 GB | approximately 387 GB extracted | 64 GB starting point with splitting; 400+ GB maximizes throughput | None |
+| GigaRef singleton GPU MMseqs | 189.12 GB | approximately 395 GB extracted | 64 GB starting point with splitting; 400+ GB maximizes throughput | At least one MMseqs2-GPU-compatible NVIDIA GPU; the database need not fit VRAM |
 | 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 |
 
@@ -72,8 +80,8 @@ hf download "$REPO" --repo-type dataset --revision "$REV" \
 ```
 
 Valid FASTA targets are `gigaref-full`, `gigaref-singletons`,
-`gigaref-no-singletons`, and `uniref50`. Only
-`gigaref-no-singletons` currently has CPU and GPU MMseqs databases.
+`gigaref-no-singletons`, and `uniref50`. CPU and GPU MMseqs targets are
+`gigaref-singletons`, `gigaref-no-singletons`, and `uniref50`.
 
 ## Extract and search
 
@@ -96,8 +104,8 @@ find "mmseqs-gpu/$TARGET" -type f -name '*.gz' -print0 |
 The resulting target prefixes are:
 
 ```text
-mmseqs-cpu/gigaref-no-singletons/db/db
-mmseqs-gpu/gigaref-no-singletons/db_gpu/db_gpu
+mmseqs-cpu/$TARGET/db/db
+mmseqs-gpu/$TARGET/db_gpu/db_gpu
 ```
 
 For a 64 GB host, use native MMseqs target splitting:
@@ -111,7 +119,8 @@ mmseqs search queryDB TARGET_DB resultDB tmp \
 
 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.
+The UniRef50 and singleton databases were built directly from their published
+combined FASTAs, so their sequence identifiers match. The no-singletons FASTA
+and MMseqs database contain the same 1.8B-sequence corpus, but the FASTA uses
+`gr_<source-index>` identifiers while the existing MMseqs database retains
+older `g<part>_<row>` identifiers. This difference does not affect inference.