User: Elisabeth Gasteiger

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

<prev • 140 results • page 1 of 14 • next >
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Answer: A: Downloading all UniProt dataset
... You could download the complete flat file (either from the UniProt FTP site, or from your query result page on the website) and then use grep or some scripting language to keep only these line types. If you need assistance with regular expressions to obtain exactly this data, please don't hesitate t ...
written 1 day ago by Elisabeth Gasteiger1.2k
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Comment: C: UniProt ID mapping API call
... Just wanted to complement my colleague "me"'s reply.... (also for future readers of this thread). Glad you found your solution! ...
written 5 days ago by Elisabeth Gasteiger1.2k
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Answer: A: UniProt ID mapping API call
... UniProt IDmapping documentation for programmatic access is available here: http://www.uniprot.org/help/api_idmapping There also is a list of column names for programmatic access: http://www.uniprot.org/help/uniprotkb_column_names . In particular, for gene names, you can choose between the following ...
written 5 days ago by Elisabeth Gasteiger1.2k
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Answer: A: UniProt references to SwissProt references?
... First of all, a short note on terminology. The UniProt Knowledgebase (UniProtKB) consists of 2 section: UniProtKB/Swiss-Prot for reviewed entries and UniProtKB/TrEMBL for unreviewed entries (see http://www.uniprot.org/help/uniprotkb_sections, http://www.uniprot.org/help/entry_status). Since Swiss- ...
written 8 days ago by Elisabeth Gasteiger1.2k
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Answer: A: 3D structure for proteins
... What do your "protein names" look like? If you have UniProt accession numbers or gene names, you can use the UniProt IDmapping tool at http://www.uniprot.org/uploadlists to map your identifiers or gene names to PDB. Please don't hesitate to contact the UniProt helpdesk if you have any UniProt-speci ...
written 5 weeks ago by Elisabeth Gasteiger1.2k
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Comment: C: Batch Download Enzymes by EC Number
... Yes, this RESTful programmatic access is an approach we would have recommended at the UniProt helpdesk. See also - http://www.uniprot.org/help/api - http://www.uniprot.org/help/api_queries in case you hadn't noticed these documents yet. ...
written 11 weeks ago by Elisabeth Gasteiger1.2k
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Answer: A: How to download all the protein sequences (FASTA files) that contain a specific
... You can also try UniProt's peptide search service http://www.uniprot.org/peptidesearch, although this is using the same service as the interface you tried at U Delaware. If you have any sequences that are returned at NCBI but not by the UniProt service, it would be interesting to see examples. Data ...
written 3 months ago by Elisabeth Gasteiger1.2k
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Answer: A: how to extract protein info for a bunch of IDs
... If your problem is obtaining the FASTA format for many UniProtKB identifiers at one, rather than downloading it one by one, you can use the batch retrieval service at http://www.uniprot.org/uploadlists Please don't hesitate to contact the UniProt helpdesk in case of doubts. We try to monitor questi ...
written 4 months ago by Elisabeth Gasteiger1.2k
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Answer: A: Perl script to retrieve species name from Swissprot
... This doesn't really answer your question, but you could also have a look at the Swissknife PERL package, http://swissknife.sourceforge.net/docs/ ...
written 4 months ago by Elisabeth Gasteiger1.2k
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Answer: A: How to measure the quality of a predicted protein?
... Have you tried this? https://cameo3d.org/ CAMEO continuously evaluate the accuracy and reliability of predictions ...
written 4 months ago by Elisabeth Gasteiger1.2k

Latest awards to Elisabeth Gasteiger

Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Scholar 5 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Guru 10 months ago, received more than 100 upvotes.
Popular Question 10 months ago, created a question with more than 1,000 views. For Uniprotkb Accession Number Format To Be Extended To 10 Characters
Scholar 11 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
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Appreciated 17 months ago, created a post with more than 5 votes. For C: Proteins without genes ? Is that even possible ?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Scholar 18 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Scholar 19 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Scholar 2.1 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Scholar 2.3 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Scholar 2.6 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Scholar 2.7 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: Proteins without genes ? Is that even possible ?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Scholar 2.8 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
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Good Answer 6.0 years ago, created an answer that was upvoted at least 5 times. For A: Isoforms Missing In Uniprot Isoforms Fasta File

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