User: Elisabeth Gasteiger

Reputation:
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Location:
Geneva
Website:
http://www.uniprot.org/
Last seen:
1 week, 6 days ago
Joined:
6 years, 7 months ago
Email:
e******************@gmail.com

Posts by Elisabeth Gasteiger

<prev • 157 results • page 1 of 16 • next >
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Comment: C: Creation of UniProt Pseudo-metagenome
... Please consider adding tags "uniprot" and "protein" to your post. ...
written 18 days ago by Elisabeth Gasteiger1.4k
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Answer: A: mRNA to protein
... For a simple interactive tool, you may also try ExPASy's Translate tool (https://web.expasy.org/translate) - there is a new beta version available right now, waiting for feedback. ...
written 25 days ago by Elisabeth Gasteiger1.4k
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Comment: C: eggNOG - extracting orthologous sequences
... Apologies for not replying sooner. As you have probably found out since you wrote this, UniProtKB is indeed not at all limited to human proteins, but currently holds sequences from more than 600,000 taxons, cf https://www.uniprot.org/taxonomy/?query=rank:species&fil=annotated%3Ayes&sort=scor ...
written 25 days ago by Elisabeth Gasteiger1.4k
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Answer: A: eggNOG - extracting orthologous sequences
... I cannot reply for eggNOG, but as a side note: UniProtKB has cross-references to eggNOG and other phylogenomic databases. e.g. https://www.uniprot.org/uniprot/P01112#family_and_domains You could pick an identifier from one of these cross-references and then query UniProtKB (also possible via the R ...
written 7 weeks ago by Elisabeth Gasteiger1.4k
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Answer: A: How to parse a dat file into FASTA format?
... I recommend that you have a look at these threads and the answers I gave there: How to makeblastdb Uniprot's Taxonomic Divisions? https://www.biostars.org/p/153531/#154847 Converting Uniprot File to a Fasta File in Perl https://www.biostars.org/p/238376/#238445 ...
written 8 weeks ago by Elisabeth Gasteiger1.4k
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Answer: A: Download genes coding for specific length of proteins
... If you want to use UniProt, you can do the following query: https://www.uniprot.org/uniprot/?query=taxonomy%3Aarthropoda%20length%3A%5B150%20TO%20*%5D&sort=score&columns=id%2Centry%20name%2Creviewed%2Cgenes%2Corganism-id%2Clength Note that the column layout can be modified (for the above UR ...
written 9 weeks ago by Elisabeth Gasteiger1.4k
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Answer: A: How to specify columns in Uniprot batch query from Uniprot IDs?
... You can try something like this below - and note that the column names are documented at https://www.uniprot.org/help/uniprotkb_column_names : use strict; use warnings; use LWP::UserAgent; my $list = $ARGV[0]; # File containg list of UniProt identifiers. my $base = 'ht ...
written 9 weeks ago by Elisabeth Gasteiger1.4k
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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 3 months ago by Elisabeth Gasteiger1.4k
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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 3 months ago by Elisabeth Gasteiger1.4k
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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 months ago by Elisabeth Gasteiger1.4k

Latest awards to Elisabeth Gasteiger

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Scholar 4 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 4 months 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 8 months ago, created an answer with at least 3 up-votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
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?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Guru 16 months ago, received more than 100 upvotes.
Popular Question 16 months ago, created a question with more than 1,000 views. For Uniprotkb Accession Number Format To Be Extended To 10 Characters
Scholar 17 months ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Centurion 23 months ago, created 100 posts.
Appreciated 23 months ago, created a post with more than 5 votes. For C: Proteins without genes ? Is that even possible ?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
Scholar 2.0 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Teacher 2.0 years 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?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Proteins without genes ? Is that even possible ?
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?
Scholar 3.0 years ago, created an answer that has been accepted. For A: How do MetaCyc and Expasy Enzyme database contents relate to each other?
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Isoforms Missing In Uniprot Isoforms Fasta File
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Isoforms Missing In Uniprot Isoforms Fasta File
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?
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Proteins without genes ? Is that even possible ?

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