Protein language model embeddings and predictions for the fly proteome (FlyBase)
<p>Residue and sequence embeddings of the fly (drosophila melanogaster) proteome (FlyBase for organism drosophila melanogaster, downloaded on 2022.03.01) computed using bio_embeddings (bioembeddings.com) using the ProtT5 embedder at full precision (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3). To open the embeddings file, please see <a href="https://github.com/sacdallago/bio_embeddings/blob/develop/notebooks/open_embedding_file.ipynb">this notebook</a>. The embeddings will be indexed by numbers according to the mapping file (mapping_file.csv) in this dataset. All following results will share the same mapping (for instance, to access the variation prediction results, by accessing index "0", you will query results for the sequence "FBpp0304622").</p>
<p>Additionally:</p>
<p>- Sequence-level predictions of subcellular localization in 10 classes using LA (https://www.biorxiv.org/content/10.1101/2021.04.25.441334v1)</p>
<p>- Residue-level three state secondary structure prediction (alpha, sheet or other) using models reported in the ProtTrans paper (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3)</p>
<p>- Residue-level prediction of conservation (in 9 states) and of variation effect (from 0 [no-effect] to 1 [effect]) using VESPAl (https://doi.org/10.1007/s00439-021-02411-y)</p>
<p> </p>
<p>Files included:</p>
<p>- dmel-all-translation-r6.44.fasta --> FASTA-formatted sequences of drosophila melanogaster from FlyBase</p>
<p>- mapping_file.csv --> A CSV file mapping the identifiers used in the following files (from 0 to 30737) to the identifiers in the FlyBase fasta file (dmel-all-translation-r6.44.fasta).</p>
<p>- DSSP3_fly_ProtT5Sec.fasta --> Secondary structure predictions in three states for each residue of each protein in dmel-all-translation-r6.44.fasta. "H" stands for Helix; "E" stands for Sheet; "C" stands for Other.</p>
<p>- subcell_fly_LA_ProtT5.csv --> Subcellular location (10 states) and memrane-boundness (2 states) for each protein in dmel-all-translation-r6.44.fasta</p>
<p>- embeddings_file.h5 --> per-residue embeddings of sequences in dmel-all-translation-r6.44.fasta. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length Lx1024, with L being the length of the protein sequence. Datasets are indexed using integers. The original sequence identifier (from the FASTA header) can be accessed through the "original_id" attribute. See https://docs.bioembeddings.com/v0.2.0/notebooks/open_embedding_file.html for information on how to open the file.</p>
<p>- reduced_embeddings_file.h5 --> per-sequence embeddings of sequences in dmel-all-translation-r6.44.fasta (obtained by mean-pooling the residue-embeddings along the length dimension of the protein sequence). Each dataset in the .h5 file represents a protein sequence and contains a vector of size 1024 (meaning, each sequence has the same dimension).</p>
<p>- conspred_probs.h5 --> per-sequence conservation probability (softmax) prediction of sequences in dmel-all-translation-r6.44.fasta in 9 classes. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length 9xL, with L being the length of the protein sequence, and 9 being the predicted conservation class (index 0 = very variable; index 8 = very conserved)</p>
<p>- vespal_SAVeffect_fly.zip --> zipped .h5 file of per-sequence variation predictions of sequences in dmel-all-translation-r6.44.fasta on a scale from 0 (neutral) to 1 (effect). -1 indicates WT substitution. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length 20xL, with L being the length of the protein sequence, and 20 being the predicted variation score for each residue substitution (AAs in the following order: "<strong>ALGVSREDTIPKFQNYMHWC</strong>" . Meaning that index 0 = substitution of the residue to "A", index = 1 substitution to residue "L", aso.)</p>
openafl-3.0Mar 2022View details →
