Entering edit mode
6.4 years ago
Kian
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50
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.
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"
in output there is:
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)
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
Select seq NM_005706.3
Select seq NM_001297659.1
Select seq NM_001297658.1