User: Elisabeth Gasteiger

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

<prev • 173 results • page 1 of 18 • next >
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Answer: A: Amino acid protein software
... You could try this tool: https://web.expasy.org/aacompident/aacomp0.html It's somewhat old, but if you specify 0% for your specific amino acid, and roughly 5% for any other amino acid, you should find some examples. ...
written 6 weeks ago by Elisabeth Gasteiger1.5k
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Answer: A: short peptide mapping to Multiple seq alignment (MSA)
... UniProt's PeptideSearch doesn't map peptides against a MSA, but can find exact peptide matches (multiple peptides can be entered simultaneously) in the UniProt Knowledgebase: https://www.uniprot.org/peptidesearch ...
written 6 weeks ago by Elisabeth Gasteiger1.5k
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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 4 months 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 4 months 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 5 months 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 6 months 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 6 months 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 7 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 8 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 8 months ago by Elisabeth Gasteiger1.5k

Latest awards to Elisabeth Gasteiger

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Welcome to the new UniProt beta site!
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
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?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Scholar 15 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: Isoforms Missing In Uniprot Isoforms Fasta File
Scholar 21 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Guru 2.2 years ago, received more than 100 upvotes.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Uniprotkb Accession Number Format To Be Extended To 10 Characters
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?
Centurion 2.7 years ago, created 100 posts.
Appreciated 2.8 years ago, created a post with more than 5 votes. For C: Proteins without genes ? Is that even possible ?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
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?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
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?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Scholar 3.4 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Scholar 3.7 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Scholar 3.9 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Good Answer 4.0 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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