User: hazirliver

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hazirliver10
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Posts by hazirliver

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to download not a whole FASTA file, but only a certain interval?
... I mean FASTA sequences that can be downloaded from ncbi. From software I will try to deal with anyone, but it will be more convenient with python/biopython or R ...
written 10 days ago by hazirliver10
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How to download from ncbi not a whole FASTA file, but only a certain interval?
... Hi! I have a list with accession numbers from ncbi and intervals i need to download. Is there a way to download not a whole FASTA file, but only a certain interval with python/biopython or R (or using some other soft)? An example list is provided below. id acc_no start stop ...
fasta R biopython genbank written 10 days ago by hazirliver10 • updated 10 days ago by genomax78k
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Comment: C: Convert huge list of accession numbers to GI numbers
... In my previous post I meant the file from the article. ...
written 10 weeks ago by hazirliver10
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Comment: C: Convert huge list of accession numbers to GI numbers
... Thanks for Entrezdirect! I think that their "gi"s aren't gi numbers in GenBank because each accession number doesn't match gi in whole file ...
written 10 weeks ago by hazirliver10
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Comment: C: Convert huge list of accession numbers to GI numbers
... https://www.nature.com/articles/s41596-019-0211-1 They use both accession numbers and gi numbers. To be more specific there are "GeneratedID"s, but in ProtocolFiles (Vicinity.faa) there are lines like ">gi|1000270263|gb|AAD36848.1| AAD36848.1 acetylornithine aminotransferase [Thermotoga maritima ...
written 10 weeks ago by hazirliver10
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Comment: C: Convert huge list of accession numbers to GI numbers
... I know it, but i can try to apply Koonin's pipepline from 2019 article in which they use gi numbers to define sequnces ...
written 10 weeks ago by hazirliver10
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Convert huge list of accession numbers to GI numbers
... Hello! I have a huge list of accession numbers (a little bit more than 1 million) and i need to get relevant gi numbers. Are there any ways to do this? ...
ncbi gi accession numbers gi numbers written 10 weeks ago by hazirliver10
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Comment: C: Update list of asseccion numbers
... Thank you! I will try to find the answer there ...
written 12 weeks ago by hazirliver10
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Update list of asseccion numbers
... Hello! I have a list with accession numbers, but some of the numbers on this list are out of date (they are "old version"). Are there any easy ways (using biopython or ready-made scripts) to update this list? ...
ncbi python biopython genbank accession number written 12 weeks ago by hazirliver10 • updated 5 weeks ago by Biostar ♦♦ 20

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