Question: How to extract a sequence of gene from UCSC table browser in specific region
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gravatar for Kian
15 months ago by
Kian40
Kian40 wrote:

Hi How to extract a sequence of gene from UCSC table browser in specific region when i want to extract sequence of a gene like TSSC4 with "chr11 2400408-2403878" region in UCSC table browser, in output there are several region including specific different region in output. I want to know how i can get only specific region sequence.

ADD COMMENTlink written 15 months ago by Kian40

See this post:

How To Get The Sequence Of A Genomic Region From Ucsc?

and its possible duplicate:

Extract A Sequence From Ucsc

What exactly did you mean by that?

"in output there are several regions including specific different region in output"

ADD REPLYlink modified 15 months ago • written 15 months ago by natasha.sernova3.4k

in output there is:

hg38_ncbiRefSeq_XM_011519830.2 range=chr11:2400409-2403878 5'pad=0 3'pad=0 strand=+ repeatMasking=none GG...

hg38_ncbiRefSeq_NM_001297661.1 range=chr11:2400488-2403878 5'pad=0 3'pad=0 strand=+ repeatMasking=none CCC...

hg38_ncbiRefSeq_NM_005706.3 range=chr11:2400488-2403878 5'pad=0 3'pad=0 strand=+ repeatMasking=none CCC...

hg38_ncbiRefSeq_NM_001297660.1 range=chr11:2400488-2403878 5'pad=0 3'pad=0 strand=+ repeatMasking=none CCC...

hg38_ncbiRefSeq_NM_001297658.1 range=chr11:2400488-2403878 5'pad=0 3'pad=0 strand=+ repeatMasking=none CC...

hg38_ncbiRefSeq_XM_006718118.2 range=chr11:2400798-2403878 5'pad=0 3'pad=0 strand=+ repeatMasking=none GGTA...

hg38_ncbiRefSeq_NM_001297659.1 range=chr11:2401018-2403878 5'pad=0 3'pad=0 strand=+ repeatMasking=none CGAG...

i want only specific region "chr11 2400408-2403878", it can result in more problem specially when i want to extract codon region of gene. the output are more.
ADD REPLYlink modified 15 months ago • written 15 months ago by Kian40

According to the Biostars' instructioms, you can do two things.

How To Get The Sequence Of A Genomic Region From Ucsc?

For example, http://togows.org/api/ucsc/hg38/chr1:12,345-12,500.fasta returns the reference genome sequence in the fasta format.

Or use table browser:

http://genome.ucsc.edu/cgi-bin/hgTables?org=human

fasta-format of your fragment looks like that:

http://togows.org/api/ucsc/hg38/chr11:2,400,408-2,403,878.fasta

This is not a format you are looking for, isn't it. Do you need to play with table browser?

See these posts below as well:

UCSC Table Browser: redundant CDS sequences in generated fasta

http://genomewiki.ucsc.edu/index.php/Programmatic_access_to_the_Genome_Browser

(the last link from the very first post)

ADD REPLYlink modified 15 months ago • written 15 months ago by natasha.sernova3.4k

Dear Kian,

I've forgotten about UCSC, took the fasta sequence and run nucleotide BLAST (Somewhat similar sequences (blastn)).

I've got a lot of information, for example, this one (see below). Are you interested in this kind of information?

Select seq NM_001297660.1

Homo sapiens tumor suppressing subtransferable candidate 4 (TSSC4), transcript variant 4, mRNA

2291    3406    54%     0.0 100%    NM_001297660.1

Select seq NM_005706.3

Homo sapiens tumor suppressing subtransferable candidate 4 (TSSC4), transcript variant 3, mRNA

2291    3145    50%     0.0 100%    NM_005706.3

Select seq NM_001297659.1

Homo sapiens tumor suppressing subtransferable candidate 4 (TSSC4), transcript variant 2, mRNA

2291    3430    54%     0.0 100%    NM_001297659.1

Select seq NM_001297658.1

Homo sapiens tumor suppressing subtransferable candidate 4 (TSSC4), transcript variant 1, mRNA

2291    3709    59%     0.0 100%    NM_001297658.1
ADD REPLYlink modified 15 months ago • written 15 months ago by natasha.sernova3.4k
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