Finding S. cerevisiae mRNA of specific genes from SGD db.

Question

[elisheva]

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!!

[GenoMax]

What do you mean you can't download sequence from SGD (e.g. YAL063C which is also called FLO9).

[elisheva]

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.

Answer 1

[GenoMax]

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

[elisheva]

Thanks a lot.
I am not familiar with this tool.
How can I run it from the command line? I can't open it.

[GenoMax]

I gave you the example command line above.

[elisheva]

I know, but I am trying it and i get: Permission denied.
Should I install this tool or something like this? I downloaded it but it's a executable file.

[GenoMax]

You don't need to install since it is a stand alone executable. All you should need to do is make the file executable by doing chmod u+x faSomeRecords and then run it ./faSomeRecords orf_coding_all.fasta file_w_id extracted.fa

[elisheva]

It works now, Thanks!!