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&nbsp;2022.03.01)&nbsp;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&nbsp;<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)&nbsp;in this dataset. All following&nbsp;results will share the same mapping (for instance, to access the variation prediction results, by accessing index &quot;0&quot;, you will query results for the&nbsp;sequence &quot;FBpp0304622&quot;).</p> <p>Additionally:</p> <p>- Sequence-level&nbsp;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&nbsp;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&nbsp;(https://doi.org/10.1007/s00439-021-02411-y)</p> <p>&nbsp;</p> <p>Files included:</p> <p>- dmel-all-translation-r6.44.fasta --&gt; FASTA-formatted sequences of drosophila melanogaster from FlyBase</p> <p>- mapping_file.csv --&gt; A CSV file mapping the identifiers used in the following files (from 0 to&nbsp;30737) to the identifiers in the FlyBase fasta file (dmel-all-translation-r6.44.fasta).</p> <p>-&nbsp;DSSP3_fly_ProtT5Sec.fasta --&gt; Secondary structure predictions in three states for each residue of each protein&nbsp;in dmel-all-translation-r6.44.fasta. &quot;H&quot; stands for Helix; &quot;E&quot; stands for Sheet; &quot;C&quot; stands for Other.</p> <p>-&nbsp;subcell_fly_LA_ProtT5.csv --&gt; Subcellular location (10 states) and memrane-boundness (2 states)&nbsp;for each protein in dmel-all-translation-r6.44.fasta</p> <p>-&nbsp;embeddings_file.h5 --&gt; per-residue embeddings of sequences in dmel-all-translation-r6.44.fasta. Each dataset&nbsp;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 &quot;original_id&quot; attribute. See&nbsp;https://docs.bioembeddings.com/v0.2.0/notebooks/open_embedding_file.html for information on how to open the file.</p> <p>-&nbsp;reduced_embeddings_file.h5 --&gt; 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&nbsp;in the .h5 file represents a protein sequence and contains a vector of size 1024 (meaning, each sequence has the same dimension).</p> <p>-&nbsp;conspred_probs.h5 --&gt; per-sequence conservation probability (softmax) prediction of sequences in dmel-all-translation-r6.44.fasta in 9 classes. Each dataset&nbsp;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>-&nbsp;vespal_SAVeffect_fly.zip --&gt; zipped .h5 file of per-sequence variation predictions&nbsp;of sequences in dmel-all-translation-r6.44.fasta on a scale from 0 (neutral) to 1 (effect). -1 indicates WT substitution.&nbsp;Each dataset&nbsp;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&nbsp;being the predicted variation score for each residue substitution&nbsp;(AAs in the following order: &quot;<strong>ALGVSREDTIPKFQNYMHWC</strong>&quot; . Meaning that index 0 = substitution of the residue to &quot;A&quot;, index = 1 substitution to residue &quot;L&quot;, aso.)</p>