User: Elisabeth Gasteiger

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http://www.uniprot.org/
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Posts by Elisabeth Gasteiger

<prev • 171 results • page 1 of 18 • next >
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Comment: C: Metabolic pathways from list of protein ID numbers
... OFW53612.1 OGD16911.1 OGD16900.1 PKP54795.1 PKP54793.1 PKP58768.1 PKP59194.1 OGD17541.1 are indeed EMBL/GenBank/DDBJ CDS identifiers, and I can map them without any problem. Maybe the service wasn't functional when you tries? Can you do it now? WP_090599220.1 and WP_090721821.1 are RefSeq Protein ...
written 2 days ago by Elisabeth Gasteiger1.5k
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Comment: C: Metabolic pathways from list of protein ID numbers
... What type of NCBI IDs do you have? The UniProt IDmapping tool accepts EMBL/GenBank/DDBJ identifiers, EMBL/GenBank/DDBJ CDS (protein_ids), RefSeq and GeneID (Entrez Gene) identifiers. ...
written 19 days ago by Elisabeth Gasteiger1.5k
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News: UniProtKB: Standardization of 'Catalytic activity' annotations
... To allow [UniProt][1] to curate reactions at the level of specific enzymes instead of enzyme classes, and to use standardized names for reactants, we will use chemical reaction descriptions from the [Rhea][2] database whenever possible. For catalytic activities that can only be described in the form ...
news uniprot written 8 weeks ago by Elisabeth Gasteiger1.5k
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Answer: A: Downloading all Helix-turn-helix motif containing protein from bacteria
... You can download these proteins from UniProt (https://www.uniprot.org). For a given Pfam identifier, e.g. PF01325 use query database:(type:pfam pf01325) https://www.uniprot.org/uniprot/?query=database%3A%28type%3Apfam+PF01325%29&sort=score And then click on "Download", selecting FASTA for ...
written 9 weeks ago by Elisabeth Gasteiger1.5k
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Answer: A: Get a list of PDB id from a list of sequence protein number ?
... If your protein identifiers are from UniProtKB, you can use the UniProt IDmapping or Batch retrieve service at https://www.uniprot.org/uploadlists. You can either map from UniProtKB to PDB, or from UniProtKB to UniProtKB and then customize your results by adding a column for PDB cross-references and ...
written 12 weeks ago by Elisabeth Gasteiger1.5k
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Answer: A: Where to BLAST all characterized proteins?
... There is no magic solution since UniProtKB/Swiss-Prot is curated manually by a team of scientific biocurators (a couple of them specializing in plant biocuration) who cannot possibly keep up with the flood of uncharacterized sequence from genome projects. You could perform your BLAST search against ...
written 3 months ago by Elisabeth Gasteiger1.5k
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Answer: A: Extracting Sub-cellular location from Uniprot into tabular format
... It looks like you have meanwhile figured out much of the answer. Here is a summary from the UniProt point of view (all SIB employees were out of town for an instutional event for a couple of days, sorry): The "Subcellular location" section (https://www.uniprot.org/help/subcellular_location_section) ...
written 4 months ago by Elisabeth Gasteiger1.5k
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Answer: A: uniprot.org is moving from HTTP to HTTPS
... This is now effective, see https://www.uniprot.org/news/2018/06/20/release (the above URL no longer works since the announcement moved from "forthcoming changes" to "news"). Please make sure you update your code, or if you are using some third-party software affected by this redirection, contact the ...
written 4 months ago by Elisabeth Gasteiger1.5k
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News: Programmatic access uniprot.org: Deprecation of legacy REST URLs /batch and /mapping - please replace by /uploadlists
... Programmatic access to UniProt “Retrieve/IDmapping” service should be addressed to the URL path /uploadlists as shown in the code examples in the respective service help pages ID mapping and Batch retrieval. See announcement for details: https://www.uniprot.org/help/uploadlists_change /mapping and ...
news uniprot written 5 months ago by Elisabeth Gasteiger1.5k
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Comment: C: Query UniProt database with Mnemonic identifier
... You can access the UniProt Batch retrieval/IDmapping service (https://www.uniprot.org/uploadlists) programmatically, too, cf https://www.uniprot.org/help/api_batch_retrieval and https://www.uniprot.org/help/api_idmapping for code examples. Please note however that the /mapping service will be depre ...
written 5 months ago by Elisabeth Gasteiger1.5k

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Popular Question 23 months ago, created a question with more than 1,000 views. For Uniprotkb Accession Number Format To Be Extended To 10 Characters
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