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2 results for “DPCfam”
Unified Human Gastrointestinal Proteome clustering results by DPCfam
<p>This dataset contains the result of clustering the Unified Human Gastrointestinal Proteome (UHGP) using the DPCfam algorithm. </p> <p>More details on the DPCfam clustering algorithm can be found in the original publication:</p> <p>Russo, Elena Tea, et al. "DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets." <em>PLOS Computational Biology</em> 18.10 (2022): e1010610. <a href="https://doi.org/10.1371/journal.pcbi.1010610">https://doi.org/10.1371/journal.pcbi.1010610</a></p> <p>All of the putative protein families obtained through DPCfam (including previous results) can be browsed online at our dedicated webserver: <a href="https://dpcfam.areasciencepark.it/uhgp">https://dpcfam.areasciencepark.it/uhgp</a></p> <p>The original protein dataset is version 1.0 of the UHGP-50 dataset, available for download from MGnify at <a href="https://www.ebi.ac.uk/metagenomics/.">https://www.ebi.ac.uk/metagenomics/</a>.</p> <p><strong>FILES DESCRIPTION:</strong></p> <p>Only MCs with seeds with 1) more than 50 elements and 2) average length larger than 50 aminoacids are reported.</p> <p><strong>metaclusters_xml.tar.gz:</strong></p> <ul> <li><strong>dpcfam_uhgp_metaclusters.xml</strong>: Metaclusters' seeds. Metaclusters entries include also some statistical information about each MC (such as size, average length, low complexity fraction, etc.) and Pfam comparison (Dominant Architecture).</li> <li><strong>dpcfam_metaclusters.xsd</strong>: XML schema file for the data. </li> <li><strong>MCxml_to_tables.awk:</strong> Awk script to convert from XML to tabular text files. Use through the parse.sh script.</li> <li><strong>parse.sh</strong>: XML parser. </li> <li><strong>README.md</strong></li> </ul> <p><strong>uhgp_xml.tar.gz: </strong></p> <ul> <li><strong>uhgp_seed_match.xml</strong>: XML file containing all of UHGP-50 proteins and its corresponding sequences, annotated with Pfam and DPCfam metacluster data. Annotations comprise the membership of a protein as a seed or matches found though the profile-hmms of the DPCfam-UHGP and the DPCfam-Uniref clusterings. </li> <li><strong>uhgp_matches.xsd</strong>: XML schema file for the data. </li> <li><strong>xml_to_list.awk:</strong> Awk script to convert from XML to tabular text files. Use through the parse.sh script.</li> <li><strong>xml_to_list_mcfiles.awk:</strong> Awk script to convert from XML to tabular text files (including individual files for metaclusters' seeds). Use through the parse.sh script.</li> <li><strong>parse.sh</strong>: XML parser. </li> <li><strong>README.md</strong></li> </ul> <p><strong>Metacluster Files:</strong></p> <ul> <li><strong>seeds.zip: </strong>Metaclusters' seed sequences. A fasta file for each metacluster before filtering.</li> <li><strong>filtered_seeds.zip: </strong>Metaclusters' seed sequences after clustering at 60 percent identity. </li> <li><strong>metaclusters_hmms.tar.gz: </strong>Metaclusters' profile-hmms. A ".hmm" file for each metacluser. </li> <li><strong>metaclusters_msas.tar.gz: </strong>Metaclusters' multiple sequence alignments, in fasta format. </li> </ul> <p><strong>uhgp_protein_mapping.txt:</strong></p> <ul> <li>Contains a mapping between the identifiers of versions 1.0 and 2.0.2 of UHGP. The first column corresponds to the ID in UHGP-50 1.0 (representatives for the clustering at 50% protein identity), the second column to the ID in version 2.0.2 and the third column to the ID of the representative of the protein for clustering at 100% sequence identity, for which the protein sequence can be found in UHGP-100. </li> </ul>
Metaclusters by DPCfam clustering of UniRef50 v 2017_07
<p>Metaclusters obtained from the DPCfam clustering of UniRef50, v. 2017_07.<br> Metaclusters represent putative protein families automatically derived using the DPCfam method, as described in <em>Unsupervised protein family classification by Density Peak clustering, Russo ET, 2020, PhD Thesis <a href="http://hdl.handle.net/20.500.11767/116345">http://hdl.handle.net/20.500.11767/116345</a> . Supervisors: Alessandro Laio, Marco Punta.</em></p> <p>Visit also <a href="https://dpcfam.areasciencepark.it/">https://dpcfam.areasciencepark.it/</a> to easily navigate the data.</p> <p><strong>VERSION 1.1 changes:</strong></p> <ul> <li>Added DPCfamB database, including all small metaclusters with 25<=N<50 seed sequences. DPCdamB files are named with the prefix B_</li> <li>Added Alphafold representative based on AlphaFoldDB for each MC</li> </ul> <p><strong>FILES DESCRIPTION:</strong></p> <p><strong>1) Standard DPCfam database</strong></p> <ul> <li><strong>metaclusters_xml.tar.gz </strong>Metaclusters' seeds, unaligned in an xml table. Only MCs with seeds with 1) more than 50 elements and 2) average length larger than 50 a.a.s are reported. Metaclusters entries include also some statistical information about each MC (such as size, average length, low complexity fraction etc, ) and Pfam comparison (Dominant Architecture). A README file is included describing the data. A parser is included to transform XML data to space-separated tables. XML schema is included.</li> <li><strong>metaclusters_msas.tar.gz</strong> Metsclusters' multiple sequence alignments, in fasta format. Only MCs with seeds with 1) more than 50 elements and 2) average length larger than 50 a.a.s are reported .</li> <li><strong>metaclusters_hmms.tar.gz</strong> Metsclusters' profile-hmms. A ".hmm" file for each metacluser. Only MCs with seeds with 1) more than 50 elements and 2) average length larger than 50 a.a.s are reported .</li> <li><strong>all_metaclusters_hmm.tar.gz</strong> Collctive metaclusters' profile-hmm. A single .hmm file collecting all MC's profile-hmm. . Only MCs with seeds with 1) more than 50 elements and 2) average length larger than 50 a.a.s are reported </li> <li><strong>uniref50_annotated.xml.gz</strong> UniRef50 v.2017_07 database annotated with Pfam families and DPCfam metaclusters. A README file is included describing the data. A parser is included to transform XML data to space-separated tables. XML schema is included. XML schema is derived from uniprot's UniRef50 xml schema.</li> </ul> <p><strong>2) DPCfamB database</strong></p> <ul> <li><strong>B_metaclusters_xml.tar.gz </strong>Metaclusters' seeds, unaligned in an xml table. All metaclusters are listed. Metaclusters entries include also some statistical information about each MC (such as size, average length, low complexity fraction etc, ) and Pfam comparison (Dominant Architecture). A README file is included describing the data. A parser is included to transform XML data to space-separated tables. XML schema is included. </li> <li><strong>B_metaclusters_msas.tar.gz</strong> Metsclusters' multiple sequence alignments, in fasta format. Only MCs with seeds with 1) 25<=N<50 elements and 2) average length larger than 50 a.a.s are reported .</li> <li><strong>B_metaclusters_hmms.tar.gz</strong> Metsclusters' profile-hmms. A ".hmm" file for each metacluser. Only MCs with seeds with 1) 25<=N<50 elements and 2) average length larger than 50 a.a.s are reported .</li> <li><strong>B_ all_metaclusters_hmm.tar.gz</strong> Collctive metaclusters' profile-hmm. A single .hmm file collecting all MC's profile-hmm. . Only MCs with seeds with 1) 25<=N<50 elements and 2) average length larger than 50 a.a.s are reported </li> </ul> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
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