User: Elisabeth Gasteiger

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Geneva
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http://www.uniprot.org/
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1 week ago
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6 years, 4 months ago
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Posts by Elisabeth Gasteiger

<prev • 150 results • page 1 of 15 • next >
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Comment: C: How to convert bulk UniProt Id to GO terms/Ids?
... I'm afraid I don't quite understand what you are trying to do. What is your input? Please don't hesitate to contact the UniProt helpdesk with your question (or open a new thread in BioStars). ...
written 8 days ago by Elisabeth Gasteiger1.3k
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Answer: A: How to retrieve single protein fasta file for multiple species?
... If you are working with UniProt, you can retrieve the data programmatically as described here (with code examples): https://www.uniprot.org/help/api_downloading https://www.uniprot.org/help/api_queries ...
written 10 days ago by Elisabeth Gasteiger1.3k
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Answer: A: how to get protparam physico and chemical properties for each sequence using per
... There isn't a very sophisticated way of accessing ProtParam programmatically, but you can send GET requests such as https://web.expasy.org/cgi-bin/protparam/protparam1/?P15457@noft@ (for UniProtKB accession P15457) https://web.expasy.org/cgi-bin/protparam/protparam/?sequence=ASADSDFSF (for raw sequ ...
written 4 weeks ago by Elisabeth Gasteiger1.3k
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Answer: A: Batch download UniProt proteomes with list of proteome IDs
... You can do this programmatically using URLs like https://www.uniprot.org/uniprot/?query=proteome:UP000005640&format=fasta (FASTA format) Use format=txt, format=xml etc for other download formats. There is a related FAQ for programmatic access with a code example to download the UniProt referen ...
written 5 weeks ago by Elisabeth Gasteiger1.3k
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Answer: A: Cross-reference with PDB database
... Here is the list of UniProtKB entries cross-referenced to PDB https://www.uniprot.org/uniprot/?query=database:(type:pdb)&format=tab&columns=id,entry%20name,reviewed,database(PDB) For reviewed entries only, you can also have a look at this precomputed file: ftp://ftp.uniprot.org/pub/database ...
written 6 weeks ago by Elisabeth Gasteiger1.3k
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Answer: A: How to not get an overcounting of proteins sequences in database ?
... Have you read the README file in the top-level directory? ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/README In the reference_proteome directory, we have attempted to *automatically* split all reference proteomes into 2 sets, the so-called "canonic ...
written 6 weeks ago by Elisabeth Gasteiger1.3k
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News: UniProtKB FASTA headers: Addition of NCBI taxonomy identifier
... In order to avoid ambiguities and simplify parsing, the NCBI taxonomy identifier will be added to UniProtKB FASTA headers. Current format: >db|UniqueIdentifier|EntryName ProteinName OS=OrganismName [GN=GeneName ]PE=ProteinExistence SV=SequenceVersion New format: >db|UniqueIdentifie ...
fasta news taxonomy uniprot swiss-prot written 8 weeks ago by Elisabeth Gasteiger1.3k • updated 8 weeks ago by GenoMax42k
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News: uniprot.org is moving from HTTP to HTTPS
... UniProt is moving web pages and services from HTTP to HTTPS: We will support separate HTTP and HTTPS services until release 2018_06 (June 20, 2018). From this date, the HTTP traffic will be automatically redirected to HTTPS. We intend to maintain these redirects indefinitely, but it is to your adva ...
database protein news uniprot written 8 weeks ago by Elisabeth Gasteiger1.3k • updated 8 weeks ago by GenoMax42k
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Answer: A: Proteins that cannot form biofilm?
... I cannot answer about the best GO terms to use, and do not know how consistently they are applied to proteins that actually form biofilm. However, from the UniProt point of view, I'd like to alert you to fact that negative queries should be used with extreme caution: Indeed, the absence of an annot ...
written 12 weeks ago by Elisabeth Gasteiger1.3k
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Answer: A: Accessing UNIPROT using REST API
... The UniProt IDmapping doesn't actually support EC numbers. For performance reasons, databases where the mapping relationship to UniProtKB identifiers is one-to-many, e.g. GO, InterPro or PubMed, are not supported. There is a note about this in the help page http://www.uniprot.org/help/uploadlists. ...
written 12 weeks ago by Elisabeth Gasteiger1.3k

Latest awards to Elisabeth Gasteiger

Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Scholar 5 weeks ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Scholar 11 weeks ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Scholar 8 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Guru 13 months ago, received more than 100 upvotes.
Popular Question 14 months ago, created a question with more than 1,000 views. For Uniprotkb Accession Number Format To Be Extended To 10 Characters
Scholar 14 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Centurion 20 months ago, created 100 posts.
Appreciated 20 months ago, created a post with more than 5 votes. For C: Proteins without genes ? Is that even possible ?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Scholar 22 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Scholar 22 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
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?
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?
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Scholar 2.9 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Proteins without genes ? Is that even possible ?

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