User: pb

gravatar for pb
pb20
Reputation:
20
Status:
New User
Location:
Canada
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Google Scholar Page
Last seen:
an hour ago
Joined:
2 years, 4 months ago
Email:
b**********@gmail.com

Posts by pb

<prev • 27 results • page 1 of 3 • next >
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Answer: A: Extracting protein sequences of enzymes for specific pathways from KEGG
... I don't know there is any tool exist to do that but if you can write your own program (python) then you will able to do that. When you open KEGG pathway (show pathway option), you can scrap that HTML page and you will find the link for every enzyme associated with that particular pathway. From that ...
written 3 months ago by pb20
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Comment: C: Getting Protein GIs from a Nucleotide Range
... Seems like your example GI number belongs to EMBL id. [EBI id map tool][1] [1]: http://www.ebi.ac.uk/Tools/picr/search.do ...
written 5 months ago by pb20
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Comment: C: String Database download data including interactions
... If you want to download interaction data for specific protein then you can use their [API service][1] [1]: http://string-db.org/cgi/help.pl? ...
written 6 months ago by pb20
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Comment: C: format uniprot fasta headers
... In this case, I would make it little easier for User using BioPython module: from Bio import SeqIO for seq_record in SeqIO.parse('sample.fasta', 'fasta'): header = seq_record.id UniprotID ='>'+str(header.split('|')[1]) ProteinName='>'+str((header.split('|')[-1]).spli ...
written 6 months ago by pb20
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Answer: A: Parsing FASTA file using class in Python
... Hi you can try my following code to generate your result: > from Bio import SeqIO seqdic={} with open('sample.fa', 'r') as input_fasta_file: for seq_record in SeqIO.parse(input_fasta_file, 'fasta'): header = seq_record.id ...
written 8 months ago by pb20
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Answer: A: How to convert bulk UniProt Id to GO terms/Ids?
... You can also use [EBI QuickGO][1] tools to fetch GO terms/ID programmatically. [1]: https://www.ebi.ac.uk/QuickGO/ ...
written 8 months ago by pb20
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Comment: C: Protein secondary structure prediction tool recommandation
... Did you try to run PSIPRED because they have the option to predict secondary structure with homology and without homology? ...
written 8 months ago by pb20
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Comment: C: How to convert a URL into a DOI programmatically
... Hi I am not sure how good you are in programming (java/python) but if you are confident enough then you can write your own code to extract DOI using following conditions: 1. If you have URL address of your article then you need to get the TITLE using web page scrapping technique(it is very easy to ...
written 13 months ago by pb20
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Comment: C: Matching Uniprot position to Pfam HMM position
... Normally if you run Pfam locally, you will get Pfam domain results for your query proteins where Pfam will display your UniProt id and domain position (start and end). Now if you want to see whether your residue present in domain regions then you can write your script to get what you want!! ...
written 14 months ago by pb20
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Comment: C: beta-sheet information from pdb file
... Yes, you can write your own python script to get the result. For more information please visit their webpage and you will get more idea. ...
written 14 months ago by pb20

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For How To Become A NGS bioinformatics expert from Protein Bioinformatician? - Skills
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