Hey Ruchi thanx for detailed explanation :) cheers Gireesh On Sat, Sep 18, 2010 at 10:46 PM, Ruchi Bajpai <rbajpai@stanford.edu> wrote:
Hey Gireesh,
The sequences are not just reverse but reverse complement, AND they are written ONLY in the 5' to 3' direction.
Taking the example of the first 16 bases ( in red) are the reverse complement of the last 16 ( in pink).
5'-3':TTCATGTTTTAACACT 5'-3':AGTGTTAAAACATGAA
Now flip the lower sequence around ( write is 3'-5' direction) and the beauty of the DNA strand becomes obvious with A's pairing with T and G with C
5'-3':TTCATGTTTTAACACT 3'-5':AAGTACAAAATTGTGA
On Fri, Sep 17, 2010 at 7:08 PM, John McPherson <John.McPherson@oicr.on.ca
wrote:
I think that you have extracted the “+” strand for your comparison. Below is the “-” strand from UCSC hg18
hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=+ repeatMasking=lower TTCATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGAAGGCATGGT TCGTAAGGCATGGGGTCTGGAGAAAAAACAGAATCATCTCCTGAAGAACA AGAACTTCTTGTGTCAGGGTAACTAGGTGAATACTGTTCGAGAGGTTGGC TGAGGTCCAAGTATTC
hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=- repeatMasking=lower GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC AGTGTTAAAACATGAA
On Sep 17, 2010, at 5:52 PM, gireesh bogu wrote:
No I extrcated -. But your sense antisense sequences should be the same but in reverse right? But your two sequences are completely different ? Why is that?
On Fri, Sep 17, 2010 at 7:08 PM, John McPherson <John.McPherson@oicr.on.ca
wrote:
I think that you have extracted the “+” strand for your comparison. Below is the “-” strand from UCSC hg18
hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=+ repeatMasking=lower TTCATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGAAGGCATGGT TCGTAAGGCATGGGGTCTGGAGAAAAAACAGAATCATCTCCTGAAGAACA AGAACTTCTTGTGTCAGGGTAACTAGGTGAATACTGTTCGAGAGGTTGGC TGAGGTCCAAGTATTC
hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=- repeatMasking=lower GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC
AGTGTTAAAACATGAA
On 10-09-16 11:28 PM, "gireesh bogu" <gireeshkbogu@gmail.com> wrote:
Dear Galaxy
I found a bug in extracting FATSA sequence tool in galaxy.
I extracted sequence of this location chr10 123229360 123229525 fgfr2 0 -
hg18_chr10_123229360_123229525_- GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC AGTGTTAAAACATGA
And I checked back in UCSC browser by pasting the same location. The sequences are completely different (hg18).
Could you please help me in this issue
Thanx Gireesh
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