User: ahir29

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ahir290
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Posts by ahir29

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NCBI Entrez not returning the correct DNA sequence for all entries
... I wrote a python definition that accepts a multi-fasta file (usually after performing a blast search and downloading the fasta file of all the hits) and basically searches the "identical protein groups" database at ncbi, finds the corresponding "nuccore" database accession number, and the start and ...
ncbi sequence retrieval entrez written 13 hours ago by ahir290 • updated 12 hours ago by piet1.5k
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Comment: C: Python Programmatically obtaining the corresponding wildtype DNA sequence of a R
... Yup, i see the same thing. You are right, I am find the etuils hit and miss. I am resorting to webscraping the ipg page now. No other choice. ...
written 9 weeks ago by ahir290
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Comment: C: Python Programmatically obtaining the corresponding wildtype DNA sequence of a R
... Is there no way to use the Entrez utils wrapper in biopython to access the "identical proteins" link ? I.e for https://www.ncbi.nlm.nih.gov/protein/WP_010594839.1 ; this would lead to "https://www.ncbi.nlm.nih.gov/ipg/?term=WP_010594839.1" ; where any of the entries there gets me to a page which has ...
written 10 weeks ago by ahir290
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Comment: C: Python Programmatically obtaining the corresponding wildtype DNA sequence of a R
... Thanks genomax - I cant believe my vigilant googling didnt get me to that page explaining where all the transcripts of a reference seq is kept! Need to improve my searching skills:) I am assuming now using the Entrez etuils wrapper in Biopython can get me the necessary transcripts. I will take a loo ...
written 10 weeks ago by ahir290
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Python Programmatically obtaining the corresponding wildtype DNA sequence of a RefSeq Protein Identifier (e.g WP_016693432.1)
... Dear All, The question is quite self explanatory - what is the easiest way (using python) to get the corresponding DNA sequence from which the translated protein sequence is available in the RefSeq NCBI database. For example, I have a fasta file after a blast search - >WP_010594 ...
database refseq mapping transcript dna written 10 weeks ago by ahir290 • updated 10 weeks ago by genomax57k

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