User: Sanjarbek Hudaiberdiev

Reputation:
50
Status:
New User
Location:
Trieste, Italy
Last seen:
2 days, 11 hours ago
Joined:
4 years, 1 month ago
Email:
o*******@gmail.com

I'm a PhD student in Bioinformatics, of CS background.

Posts by Sanjarbek Hudaiberdiev

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Edit Seq object with Biopython
... for sequence in sequences: sequence.seq = sequence.seq[10:-10] ...
written 6 months ago by Sanjarbek Hudaiberdiev50
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Answer: A: Fetching Genbank Entries For List Of Accession Numbers.
... The script provided by Leszek solves the problem. ...
written 3.8 years ago by Sanjarbek Hudaiberdiev50
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... This works fantastic! Just couldn't think myself of searching by accessions and getting ['IdList'] back. Thanks Leszek. ...
written 3.8 years ago by Sanjarbek Hudaiberdiev50
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... Any suggestions on how to download the whole data of genbank? ...
written 4.0 years ago by Sanjarbek Hudaiberdiev50
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... I usually use this way. But it's extremely slow when you want to download thousands of entries and sometimes falls to timeout. Using epost would be much better. But, apparently there's no way of doing that. ...
written 4.0 years ago by Sanjarbek Hudaiberdiev50
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... One more thing that I noticed today: All the BioXXX libraries just stop when they get error from epost. But I noticed that along with error, epost still returns WebEnv and query_key. But what it does is that, it takes the accession number, trims out the non-numeric characters, and searches for resul ...
written 4.1 years ago by Sanjarbek Hudaiberdiev50
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... Ex: A22237,A22239,A32021,A32022,A33397 Those are accessions from NCBI. When you post them using epost, it gives this error: "IDs contain invalid characters which was treated as delimiters." So it appears to me that epost doesn't accept non-numeric characters for ID field. I tried to change the ...
written 4.1 years ago by Sanjarbek Hudaiberdiev50
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... 1) Yes, I like very much working with E-utils. It's the first time I got stuck with a problem. 2) True. There's no problem in fetching by accession number in one-request-at-a-time manner. But it's slow, due to 1/3 seconds limitation of NCBI. The problem comes when you want to try epost for batch dow ...
written 4.1 years ago by Sanjarbek Hudaiberdiev50
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... I had a look on that thread. The problem is not solved there. If I had GIDs first, and wanted to convert them to Accessions, then that would be viable via epost-efetch:). But can't do the other way around. Thank you for your suggestions. ...
written 4.1 years ago by Sanjarbek Hudaiberdiev50
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... I'm working with GenBank. So, I need to map Genbank accession numbers to Genbank GI number. DAVID can't find the majority of the accessions that I submit. Moreover, it doesn't provide API, afaik. ...
written 4.1 years ago by Sanjarbek Hudaiberdiev50

Latest awards to Sanjarbek Hudaiberdiev

Student 19 days ago, asked a question with at least 3 up-votes. For Fetching Genbank Entries For List Of Accession Numbers.
Epic Question 5 months ago, created a question with more than 10,000 views. For Fetching Genbank Entries For List Of Accession Numbers.
Great Question 3.1 years ago, created a question with more than 5,000 views. For Fetching Genbank Entries For List Of Accession Numbers.
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Fetching Genbank Entries For List Of Accession Numbers.

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