User: vkkodali

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vkkodali860
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860
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United States
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an hour ago
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2 years, 5 months ago
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Posts by vkkodali

<prev • 96 results • page 2 of 10 • next >
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Answer: A: Retrieving domain loci
... Conserved domains are annotated on the RefSeq proteins. If you are starting with NCBI GeneIDs, then you may want to first fetch the proteins annotated on that gene and then extract the CDD domains for each protein. You can use [Entrez Direct](bit.ly/entrez-direct) for this as follows: elink -db g ...
written 10 days ago by vkkodali860
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Comment: C: How to extract mitogenomes from these fasta files? HELP
... Can you post example contents of the files `*.namelist`? ...
written 11 days ago by vkkodali860
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Comment: C: reterive data from UniProt
... If you manage to get the code shown above to run, there won't be any output printed to screen. The data retrieved from UniProt will be saved in the variable `entries`. If you are on the python interpreter, try this: >>> entries 'P28482\tMK01_HUMAN\tMAPK1 ERK2 PRKM1 PRKM2\n' ...
written 13 days ago by vkkodali860
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Comment: C: UniProtKB - mapping gene name to ID (*_HUMAN ) using python2
... Without more detailed information from you, I cannot be of much help. What have you tried? How did you run the code? Did you run it as a script? Or did you run it at the python interpreter? Did you use the example posted here or did you use your own example? I am not sure what you mean by 'does not ...
written 13 days ago by vkkodali860
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Comment: C: UniProtKB - mapping gene name to ID (*_HUMAN ) using python2
... Python seems to be complaining about indentation. If you have copy/pasted the code from above, you should make sure the indentation is correct. I don't think you need to indent the entire code block after the `import` statement. ...
written 13 days ago by vkkodali860
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Comment: C: Get just GenBank record while downloading genome with Biopython
... > I'm implementing a for loop to iterate into downloaded records to cut off sequence free files. Change your `rettype` to `gbwithparts` and all RefSeq flatfiles will be downloaded with contig sequences. ...
written 16 days ago by vkkodali860
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Answer: A: Get just GenBank record while downloading genome with Biopython
... Change your `search_term` to include GenBank or RefSeq filter as shown below for GenBank and RefSeq sequences, respectively ## GenBank sequences only search_term = "Bifidobacterium+bifidum+PRL2010[organism] AND complete+genome[title] AND genbank[filter]" ## RefSeq sequences only sea ...
written 16 days ago by vkkodali860
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Comment: C: uniprot protein information about reactions
... Have you used the UniProt REST API before? One of the [options](https://www.uniprot.org/help/api_queries) there is to specify which `columns` you want. In your case, you should have `ec` in addition to other columns such as `id` and `entry name`. Read up on their API at the link shown above and post ...
written 29 days ago by vkkodali860
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Comment: C: uniprot protein information about reactions
... The assumption I am making here is that the protein is an enzyme if there is an EC number assigned to it. Out of the ~15000 hits, less than 5000 are UniProt Reviewed records; which would be the only ones I'd bother to look at. Beyond that, it depends on your use case. If you need to include absolute ...
written 29 days ago by vkkodali860
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Comment: C: uniprot protein information about reactions
... What do you mean by 'it does not give anything'? I see over [15000 hits](https://www.uniprot.org/uniprot/?query=organism%3A%22Homo+sapiens+%5B9606%5D%22+ec%3A*&sort=score) returned for that query. Once you have figured out the query that you want to use, you can then proceed to use the REST API ...
written 29 days ago by vkkodali860

Latest awards to vkkodali

Scholar 6 days ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 8 days ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 8 days ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 8 days ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 4 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 4 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 4 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 4 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 8 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 10 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 10 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 10 weeks ago, created an answer that has been accepted. For C: Strange esearch behavior
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 11 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 11 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 11 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 11 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 11 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?

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