Hello, Anna,
If what you want is the sequence of the exons, there is a more
direct way than stitching together the pieces. You can use the
Table Browser. this is going to be a big operation, so I
suggest you might want to break it down by chromosome. You
will also probably want to send the output to a file, rather
than your screen (give it a filename and you will be
prompted for a directory to put it in).
Follow the "Tables" link at the top of the page in the bluebar.
select the following:
assembly: hg19
group: Genes and Gene Predictions
track: CCDS
table: ccdsGene
position: chr22 [lookup]
output format: sequence
output file: <yourFileNameChr22.exons>
[get output]
On the next page, "genomic" is your only choice.
[submit]
On the following page, check the boxes for the sequences
you want: 5'-UTR, CDS Exons, 3'-UTR ...
You can choose to stitch them together here by selecting
"One FASTA record per gene" or have it in pieces by exon.
[get sequence]
best wishes,
--b0b kuhn
ucsc genome bioinformatics group
On 3/8/2012 12:03 PM, [email protected] wrote:
> Hi,
>
> For each gene in the CCDS set from the human reference genome (NCBI build
> 37.3, hg19), the
> coordinates for each of the exons are given. I am interested in pasting
> together the sequences of all
> the exons together for each gene and translating the DNA sequence into
> protein sequence. Is there
> a way to determine what reading frame each coding sequence is in relative to
> the start of the
> transcript for each gene in the CCDS set?
>
> thanks,
> Anna
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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