User: taojincs

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taojincs10
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Posts by taojincs

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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 11 weeks ago by taojincs10
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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 11 weeks ago by taojincs10
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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 11 weeks ago by taojincs10
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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 5 months ago by taojincs10
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Comment: C: How to download COMPLETE bacterial genomes from NCBI based on list of names?
... This didn't download the fasta file in my directory. Nothing happened. Could you please double check it? ...
written 7 months ago by taojincs10
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How to download COMPLETE bacterial genomes from NCBI based on list of names?
... I have a long list of complete bacterial organism names (more than 100000, thus impossible to search and download it line by line). Format is one name on each line. I need to download GCA (It must be GCA instead of GCF) fasta files of the corresponding genomes from https://www.ncbi.nlm.nih.gov/genom ...
ncbi search written 7 months ago by taojincs10 • updated 4 months ago by arsilan32450
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about Grep the complete sequences containing a specific motif in a fasta file
... How to Grep the complete sequences containing a specific motif in a fasta file? Also, I want to include the lines beginning with a ">" before these target sequences. The image is not shown so I will add this link of example because typing > in biostar is kinda misleading: https://drive.google ...
fasta grep sequence linux written 8 months ago by taojincs10 • updated 8 months ago by Philipp Bayer5.5k
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How to download all the protein sequences (FASTA files) that contain a specific short sequence of amino acids on NCBI, such as AKIAE. How to achieve this efficiently on NCBI?
... How can I find and download all the protein sequences (FASTA files) that contain a specific short sequence of amino acids/a specific motif on NCBI, such as AKIAE. How to achieve this efficiently on NCBI? I tried http://research.bioinformatics.udel.edu/peptidematch/index.jsp http://www.genome.jp/to ...
ncbi protein written 10 months ago by taojincs10 • updated 9 months ago by Elisabeth Gasteiger1.4k

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Scholar 11 weeks ago, created an answer that has been accepted. For A: Query SwissProt using Java based on Annotation Score and Publication Number

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