Dear Sir/Madam,
Thanks for your reply. Now I like to know that in case of -ve
strand, is the DNA sequence given from the 5' end to 3' end? i.e
in -ve strand if transcription start site of a miRNA is at 1000bp
location then the sequence of 500bp upstream can be by entering
(500,1000)or(1000,1500)?
Pleaes reply at your earliest convenience.
Thanking you,
Tapas Bhadra,
Senior Research Fellow,
Indian Statistical Institute,
Kolkata,
India
> Hi Tapas,
>
> While the coordinates you specify the Get DNA utility or on the
> downloads page are always in reference to the positive strand, the DNA
> sequence is always given from the 5' end to 3' end. The correct figure
> out of the ones you gave in your email is:
>
> + strand: 1 2 3 ... x
> - strand: x ... 3 2 1
>
> I hope this information is helpful. Please feel free to contact the
> mail list again if you require further assistance.
>
> Best,
> Mary
> ------------------
> Mary Goldman
> UCSC Bioinformatics Group
>
> On 6/25/10 2:55 AM, Tapas Bhadra wrote:
>> I think there is a problem in my understanding on the numbering used
>> for base pairs in a chromosome. Can you please clarify my query? In
>> short,
>> the query is "Whether the negative strand of a chromosome is numbered in
>> ascending order just like the positive strand, or in the descending
>> order?"
>>
>> To be descriptive, the bases in the positive strand is numbered as
>> [1-2-3-...-maximum_chromosome_length]. Is the complementary negative
>> strand also numbered in databases like this or as
>> [maximum_chromosome_length- ... -3-2-1]?
>>
>> I have retrieved a sequence from the base 1 to 100 in positive
>> strand of chr 1 and also the same from negative strand and I have seen
>> that they are completely different.
>>
>> Because either the numbering is:
>> + strand: 1 2 3 ... x
>> - strand: 1 2 3 ... x
>>
>> or is:
>> + strand: 1 2 3 ... x
>> - strand: x ... 3 2 1
>>
>> Which one is correct? what are you using?
>>
>>
>>> Hi Tapas,
>>>
>>> My apologies - the browser is looking for default values to enter into
>>> the position text box. The link below should work for hg18,
>>> chr6:1000-1500:
>>>
>>> http://genome.ucsc.edu/cgi-bin/hgc?g=getDna&i=mixed&c=chr6&l=999&r=1500&db=hg18
>>>
>>> Best,
>>> Mary
>>> ---------------------
>>> Mary Goldman
>>> UCSC Bioinformatics Group
>>>
>>> On 6/24/10 4:57 PM, Tapas Bhadra wrote:
>>>
>>>> Sir,
>>>> Thanks for your reply. But when I am trying to go into the site
>>>> it
>>>> shows that "hashMustFindVal: 'c' not found " in that page.
>>>>
>>>> Pleaes reply at your earliest convenience.
>>>>
>>>> Thanking you,
>>>> Tapas Bhadra,
>>>> Senior Research Fellow,
>>>> Indian Statistical Institute,
>>>> Kolkata,
>>>> India
>>>>
>>>>
>>>>
>>>>
>>>>> Hi Tapas,
>>>>>
>>>>> Whether you obtain the DNA sequence through our downloads page or the
>>>>> "DNA" button in the blue bar when you are viewing an assembly, it
>>>>> always
>>>>> defaults to the positive strand. The easiest way to get DNA for a
>>>>> short
>>>>> sequence, such as the one you mentioned in your email, is to use the
>>>>> "get DNA" feature (http://genome.ucsc.edu/cgi-bin/hgc?g=getDna).
>>>>> Simply
>>>>> type in the coordinates and click the "get DNA" button. Note that you
>>>>> can also get DNA from the negative strand by clicking the "reverse
>>>>> complement" check box.
>>>>>
>>>>> I hope this answers this question and both of your questions that
>>>>> were
>>>>> emailed to our team yesterday. Please feel free to contact the mail
>>>>> list
>>>>> again if you require further assistance.
>>>>>
>>>>> Best,
>>>>> Mary
>>>>> ------------------
>>>>> Mary Goldman
>>>>> UCSC Bioinformatics Group
>>>>>
>>>>> On 6/24/10 4:33 AM, Tapas Bhadra wrote:
>>>>>
>>>>>
>>>>>> Dear Sir,
>>>>>> I am a research fellow at the Indian Statistical Institute,
>>>>>> Kolkata,
>>>>>> India.
>>>>>>
>>>>>> I have downloaded the sequences of all the chromosomes. Can you
>>>>>> please
>>>>>> inform me that if I need sequences from 1000bp to 1500bp of chr 6
>>>>>> from
>>>>>> +ve
>>>>>> strand and also from 1000bp to 1500bp of chr 6 from -ve strand, then
>>>>>> how
>>>>>> will I obtain those information. Will they be same?
>>>>>>
>>>>>> Is your database strand specific? If yes then which strand it
>>>>>> annotates
>>>>>> for the sequence and for this strand specific database how will we
>>>>>> obtain
>>>>>> sequential information from the reverse strand?
>>>>>>
>>>>>> Pleaes reply at your earliest convenience.
>>>>>>
>>>>>> Thanking you,
>>>>>> Tapas Bhadra,
>>>>>> Senior Research Fellow,
>>>>>> Indian Statistical
>>>>>> Institute,
>>>>>> Kolkata,
>>>>>> India
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