User: vkkodali

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vkkodali2.0k
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Posts by vkkodali

<prev • 238 results • page 1 of 24 • next >
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Comment: C: Gene starts with "LOC" prefix ?
... These don't appear to have useful gene symbols. But you can get names for these using [Entrez Direct](http://bit.ly/entrez-direct) as follows: esearch -db gene -query 'LOC117740983' | esummary | xtract -pattern DocumentSummary -element Id,Name,Description ...
written 1 day ago by vkkodali2.0k
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Comment: C: Gene starts with "LOC" prefix ?
... Can you provide an example or two? Sometimes LOCs have informative aliases that you can use. If you have the Entrez Gene IDs you can fetch a list of all aliases for each of them. ...
written 1 day ago by vkkodali2.0k
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Answer: A: How to pull metadata from SRA based on BioSample ID
... You may want to try `epost` as follows: $ cat samples.txt SAMN14390563 SAMN14390566 SAMN14390576 SAMN14390578 SAMN14453547 SAMN14453553 $ epost -db biosample -input samples.txt -format acc | \ elink -target sra | \ efetch -db sra -format runinfo -mode xml | ...
written 1 day ago by vkkodali2.0k
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Comment: C: Bioinformatics: Converting EntrezGeneID to FASTA entry for BLAST alignment
... There's [REntrez](https://cran.r-project.org/web/packages/rentrez/index.html) package that may do the trick. I haven't used it myself as much so I cannot say how well it works. ...
written 8 days ago by vkkodali2.0k
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Comment: C: How to extract CDS zones and list to an secondary text file. Perl
... Could you please provide the expected output for the protein (XP_016881659.1) in the original post? You are then starting with a GenBank flat file as input then? ...
written 8 weeks ago by vkkodali2.0k
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Comment: C: How to extract CDS zones and list to an secondary text file. Perl
... If I understand correctly, you are looking for CDS ranges. If that is all you need, you don't have to parse the GenBank flatfiles. You can get that information from GFF3 or GTF files. It appears that you are interested in human annotation. You can download the GFF3 file for the latest annotation fro ...
written 8 weeks ago by vkkodali2.0k
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Comment: C: Extract protein sequences or names based on GFF and protein file
... You can grep for protein_id and use [Entrez Direct](http://bit.ly/entrez-direct) to download protein sequences. If you have many thousands of proteins to work with and this approach is slow, you can download the protein sequences for the entire assembly separately and then use something like seqkit ...
written 8 weeks ago by vkkodali2.0k
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Comment: C: Bioinformatics: Converting EntrezGeneID to FASTA entry for BLAST alignment
... If you know which species the gene symbols are from and that they are the official symbols, you can use `esearch` with a query like this: `"Gallus gallus"[Organism] AND GJB6[Gene Name]`. Then you pipe the `esearch` results to `elink` just as above. esearch -db gene -query '"Gallus gallus"[orga ...
written 9 weeks ago by vkkodali2.0k
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Answer: A: How do I get the refseq IDs from a list of gene IDs
... You can download and parse the `gene2refseq` file from NCBI FTP site that has these mappings: https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz. If you just have a few gene IDs to work with, you can use [Entrez Direct](http://bit.ly/entrez-direct) as follows: cat gene_id_list.txt | while ...
written 9 weeks ago by vkkodali2.0k
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Comment: C: Download all bacterial genome from Refseq in fasta format from NCBI
... I believe there is no good way to do this currently. You will have to post-process your files to merge them all into a single file. If your plan is to eventually prepare a database, you can probably merge the files on-the-fly during the database prep step or somehow tell your database to read in dat ...
written 9 weeks ago by vkkodali2.0k

Latest awards to vkkodali

Scholar 20 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 9 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 3 months 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 3 months 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 3 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Scholar 5 months 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 5 months 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 6 months 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 6 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Appreciated 7 months ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Scholar 7 months 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 7 months 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 7 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Appreciated 7 months ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Teacher 7 months 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 months 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 months 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 months 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 9 months 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 9 months 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 months 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 13 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?

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