Hi everyone!
I have a problem with finding S. cerevisiae mRNA.
I have a list of genes names from SGD.
For example a few genes
Q0275
Q0297
YAL039C
YAL062W
YAL063C
And I have to download all their mRNAs into 1 fata file .
I Did it so far using RefSeq db on the table browser.
But now, because it is another db I can't just upload the list and get the mRNA as I did before.
I also tried to download from SGD coding RNA and then compare the genes Ids.
(I got the genes Ids using YeastMine)
But unfortunately these are not the same Ids.
Thanks a lot!!
1 answer
Get the sequence of all ORF's from here. Then use faSomeRecords from Kent Utilities from UCSC (with your ID's of interest in a file, one ID per line) to extract those 600 fasta files. faSomeRecords orf_coding_all.fasta file_w_id extracted.fa
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What do you mean you can't download sequence from SGD (e.g. YAL063C which is also called FLO9).
If it wasn't clear: I have a list of genes and I want to download all their mRNAs into 1 fasta file.
I'ts about 600 genes, so I can't do it manually.