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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