User: Elisabeth Gasteiger

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

<prev • 179 results • page 1 of 18 • next >
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Answer: A: uniprot variant classification DB retireve
... Are you aware of the UniProt index of human polymorphisms and disease mutations, https://www.uniprot.org/docs/humsavar ? This file lists all missense variants annotated in human UniProtKB/Swiss-Prot entries. It provides a variant classification (which is intended for research purposes only, not for ...
written 14 days ago by Elisabeth Gasteiger1.6k
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Answer: A: Which are the protein classes
... In the UniProt Knowledgebase entries, and in particular in Swiss-Prot, the reviewed section of UniProtKB, you can find a section "Sequence similarities" which contains information about sequence-based protein families to which a protein belongs. See also - https://www.uniprot.org/help/sequence_sim ...
written 7 weeks ago by Elisabeth Gasteiger1.6k
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Answer: A: Convert KEGG KO ids
... You could also use UniProt (in particular the IDmapping service at https://www.uniprot.org/uploadlists) to map your identifiers to UniProtKB and then restrict to a species (e.g. organism:9606) and possibly reviewed entries (reviewed:yes). The mapping results can be displayed in a table including gen ...
written 8 weeks ago by Elisabeth Gasteiger1.6k
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Answer: A: Is there a HGNC symbol or any ENSEMBLE/RefSeq ID for this UniProt : Rheumatoid
... According to UniProt curators, the cDNAs described in that paper (PubMed=7916589) most probably code for immunoglobulins that authors isolated as "Rheumatoid factors". They have not been manually curated in UniProtKB/Swiss-Prot for the reasons described here: https://www.uniprot.org/help/immunoglobu ...
written 10 weeks ago by Elisabeth Gasteiger1.6k
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Answer: A: Getting all ferredoxin genes/proteins from one organism
... Here is the query in UniProtKB, using InterPro IPR001080 3Fe4S_ferredoxin https://www.uniprot.org/uniprot/?query=database%3A%28type%3Ainterpro+IPR001080%29+pyrococcus&sort=score There actually seems to be only 1 entry for P.furiosus: database:(type:interpro ipr001080) AND organism:"Pyrococcus ...
written 11 weeks ago by Elisabeth Gasteiger1.6k
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Answer: A: about Java Access of Complete PubMed IDs or Titles Attached to One Entry
... I am not familiar with the EBI java API, but I may be able to shed some light on the reason why publications 7 and 8 of P0AD86 are not included: https://www.uniprot.org/uniprot/P0AD86/publications lists 8 publications, the first 6 of which have been curated by a biocurator and are actually listed i ...
written 11 weeks ago by Elisabeth Gasteiger1.6k
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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 5 months ago by Elisabeth Gasteiger1.6k
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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 5 months ago by Elisabeth Gasteiger1.6k
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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 8 months ago by Elisabeth Gasteiger1.6k
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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 8 months ago by Elisabeth Gasteiger1.6k

Latest awards to Elisabeth Gasteiger

Appreciated 5 months ago, created a post with more than 5 votes. For C: Proteins without genes ? Is that even possible ?
Popular Question 5 months ago, created a question with more than 1,000 views. For Welcome to the new UniProt beta site!
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
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Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
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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?
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Popular Question 2.6 years 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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Appreciated 3.1 years ago, created a post with more than 5 votes. For C: Proteins without genes ? Is that even possible ?
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Scholar 3.2 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 3.2 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
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?
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