Create a database of RefSeq genes

Question

[smrutimayipanda]

Hii all, I am working on microarray data analysis pipeline. I want protein coding genes, i.e all RefSeq genes of Human.to create a database. From where I can get the genes or is there any way to create a database of these genes? Please help me.

[KH]

I believe you should be able to find what you want here: https://www.ncbi.nlm.nih.gov/genome/guide/human/

You can download the file you need for either hg38 (GRCh38) or hg19 (GRCh37) human genome assemblies

[Ram]

That won't help. OP wants all protein coding sequences. Really cool resource though - I did not know that web page existed.

[smrutimayipanda]

but i need genes, not sequences. how to find that?

[smrutimayipanda]

Thank you all, the third one is working well husensofteng

[GenoMax]

smrutimayipanda : Please use ADD REPLY/ADD COMMENT when responding to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

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If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

[Ram]

smrutimayipanda, you have multiple questions that you have not accepted answers for. Please also go back and provide feedback on them.

Answer 1

[husensofteng]

The easiest way to get symbol and information on protein coding genes is through the NCBI gene resource page, here is a link for refseq protein-coding genes that you can re-generate with this query:

"Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND "srcdb refseq"[Properties] AND alive[prop])

to download the output table as a file, just click Send to: at the top of the page and select File.

Answer 2

[vkkodali_ncbi]

If you are trying to download the sequences of all protein-coding transcripts then go to this page and use the 'Download Assembly' button, choose 'RefSeq' as source and download 'RNA FASTA (.fna)' file. This has both non-coding and coding transcript sequences. You can then use seqkit to extract all protein coding transcripts as follows:

seqkit grep -r -p '[NX]M_\d+\.\d+' GCF_000001405.39_GRCh38.p13_rna.fna.gz -o protein_coding_tx.fna