User: taojincs

gravatar for taojincs
taojincs50
Reputation:
50
Status:
New User
Location:
Last seen:
1 month ago
Joined:
3 years, 6 months ago
Email:
t*******@gmail.com

Posts by taojincs

<prev • 14 results • page 1 of 2 • next >
0
votes
1
answer
253
views
1
answers
Comment: C: extract publication titles based on accession number from uniprot in python
... Thank you very much! ...
written 8 weeks ago by taojincs50
1
vote
1
answer
253
views
1
answers
Answer: A: extract publication titles based on accession number from uniprot in python
... I figured it out. Firstly, map the accession number into the entry id: https://www.uniprot.org/uploadlists/ Then, https://www.uniprot.org/help/api_retrieve_entries will help out. Both can be achieved in python. ...
written 8 weeks ago by taojincs50
2
votes
1
answer
253
views
1
answer
extract publication titles based on accession number from uniprot in python
... Is there any way to extract publication titles based on accession numbers (not UniProt identifiers) from UniProt in python? I know how to do it in Java using UniProt Java API but wonder if there is any way to do it in python. Thank you! ...
python protein uniprot written 12 weeks ago by taojincs50
0
votes
1
answer
212
views
1
answer
create sequence similarity network directly from FASTA file
... Hi everyone, I am looking for an open-source software that I can incorporate into Django or any existing tool to create sequence similarity network from FASTA file. Given several protein sequences in fasta format, it will create a network of sequence similarity with each sequence labeled. I looked ...
software similarity network protein fasta file written 4 months ago by taojincs50
2
votes
1
answer
167
views
1
answer
Tokenize FASTA Header To Separate Protein Annotation and Organism Name
... Given this fasta header as an example, ">WP_024130427.1 [50S ribosomal protein L16]-arginine 3-hydroxylase [Citrobacter koseri]", my goal is to extract accession number, protein annotation, and organism name separately. Right now, I am able to extract the accession number >WP_024130427.1 and ...
fasta protein tokenization written 4 months ago by taojincs50
0
votes
2
answers
582
views
2
answers
about Java Access of Complete PubMed IDs or Titles Attached to One Entry
... Is there any way to access ALL the publications in java attached to one swissprot entry? I know how to use the method List citation = current.getCitationsNew(). I can get the titles of these publications too. However, the list of publications is not complete. For example, https://www.uniprot.org/u ...
swissprot java api pubmed written 22 months ago by taojincs50 • updated 22 months ago by Elisabeth Gasteiger1.9k
0
votes
1
answer
770
views
1
answers
Answer: A: Query SwissProt using Java based on Annotation Score and Publication Number
... I solved this question by myself today. I knew how to do it based on https://www.ebi.ac.uk/uniprot/japi/ However, I didn't find the way to query based on annotation score. So I use Java to read the webpage source and extract that part. ...
written 2.9 years ago by taojincs50
0
votes
1
answer
770
views
1
answers
Comment: C: Query SwissProt using Java based on Annotation Score and Publication Number
... I deleted the one on the stackoverflow just now. Thank you so much for letting me know about this! ...
written 2.9 years ago by taojincs50
1
vote
1
answer
770
views
1
answer
Query SwissProt using Java based on Annotation Score and Publication Number
... I am using Java to do the query based on the protein name, the output should meet 3 conditions: 1. reviewed; 2. the annotation score >=4; 3. it has more than 3 publications related to it (the size of its PubMed ID list > 3). The output I desire is the publications related to this protein if al ...
swissprot java query protein annotation written 2.9 years ago by taojincs50
0
votes
1
answer
2.8k
views
1
answers
Comment: C: How to download COMPLETE bacterial genomes from NCBI based on list of names?
... Hi if I want to download proteomes for organisms that have been completely sequenced, should I only change "wget "$0,$NF"_genomic.fna.gz" to "wget "$0,$NF"_protein.faa.gz"? It seems what I downloaded is much larger than it should be. For example, I downloaded 11.9 GB of sequence data for 50 given or ...
written 3.2 years ago by taojincs50

Latest awards to taojincs


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2713 users visited in the last hour
_