download all gene sequences

[sinakv]

hi

I want to download all known human gene sequences available till date. Is there a way to get it? I got the list of genes from UCSC ( http://genome.ucsc.edu/knownGeneLists.html ). But how do I download the gene sequences for all of them??? Please suggest...

thanx
sina

[steven]

Go to the UCSC Table browser: http://genome.ucsc.edu/cgi-bin/hgTables?command=start
Group: genes and gene prediction tracks.
Output format: sequence.
cheers,
s.

[sinakv]

hi steven

thanx for your immediate reply....i was out of station, so couldnt reply soon.....
i had looked at the table browser option before....but in the results the gene name is not available...instead they give the code of the gene name assigned by uscs for each gene (which is mentioned in the link i posted before in this thread).....
what i require is the sequences of all the genes with the headers being their names....i also want the exons, introns, etc differentiated in the same sequence....since these are available in the database there should be an option of retrieving them easily....can u pls suggest a way....

thanx
sina

[steven]

1. Go to the UCSC Table browser: http://genome.ucsc.edu/cgi-bin/hgTables?command=start
Try it, this has nothing to do with the link you mentioned.
Select the options as shown in the attached screenshot (this is an example, you may prefer another reference annotation like UCSC or Ensembl, but make sure the assembly version is the one you need).

2. On the next screen, select "genomic" (i believe you want transcription units, not mRNA sequences) and click on "submit".

3. On the next screen you will find a wonderful interface that proposes you all the options you can dream of regarding how to retrieve your sequence (include upstream/downstream flanks, what to display in upper/lower case, etc).

Enjoy,
s.

[Joann]

thank you very much

steven,
thanks for the tip--I do not know if I am oil or water but I am planning to explore Galaxy

[sinakv]

i got it...thanks a lot steven!!!