User: Pallab Bhowmick

Reputation:
20
Status:
New User
Location:
Canada
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Google Scholar Page
Last seen:
5 hours ago
Joined:
2 years, 10 months ago
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b**********@gmail.com

Posts by Pallab Bhowmick

<prev • 28 results • page 1 of 3 • next >
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Comment: C: SIFTS (uniprot <-> pdb chain) has SP_END < SP_BEG for some mappings
... Hi did you check the .pdb file of your PDB id? DBREF section of PDB file will tell you to extract mapping of your PDB chain with corresponding Uniport sequence. DBREF 1BXH A 1 118 UNP P02866 CONA_CANEN 164 281 DBREF 1BXH A 119 237 UNP P02866 CONA_CA ...
written 4 months ago by Pallab Bhowmick20
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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 10 months ago by Pallab Bhowmick20
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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 11 months ago by Pallab Bhowmick20
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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 12 months ago by Pallab Bhowmick20
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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 13 months ago by Pallab Bhowmick20
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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 14 months ago by Pallab Bhowmick20
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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 14 months ago by Pallab Bhowmick20
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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 14 months ago by Pallab Bhowmick20
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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 20 months ago by Pallab Bhowmick20
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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 20 months ago by Pallab Bhowmick20

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Popular Question 8 months 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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