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On 8 August 2014 10:42, [email protected] <[email protected]> wrote:

> *I downloaded the file chr22.dna. I don't know what software should be
> used to browse the contents and view its data pattern. This file is really
> what I need to view its data pattern.* *Please help tell me what **software
> should be used to browse the contents.*
> *Weng*
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>
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>
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>
>
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>
>
> On Thursday, August 7, 2014 6:26:19 PM UTC-7, [email protected] wrote:
>
>> I am developing a new algorithm constructing Suffix Array that is not
>> based on KA, AS-IS or Skew algorithms. Its performance depends on Max(LCPs)
>> (the largest of longest common prefix) of the suffix array.  It will
>> work perfectly for 8-bit character string without any code change. It needs
>> some refine to deal with genome code.
>>
>> I want to know some special knowledge about genome DNA testing code. I
>> know nothing about DNA sequence and biology.
>>
>> 1. Which are the best books about genome DNA sequence processing
>> suitable for me who is developing a new algorithm constructing suffix array
>> and want the algorithm better workable for DNA analyses.
>> 2. I want to know if there is any algorithm constructing Suffix Array
>> whose performance depends on Max(LCPs)?
>> 3. Genome DNA testing file contains only 4 characters: A,C,G and T. Is
>> it right? I found another char U in RNA. Does the file still contain 4
>> characters?
>> 4. If the number of chars in a file is limited to 4, and all repeatable
>> patterns are known, I can specially design some technical refinement to
>> improve my algorithm performance. I want know, in addition to 1 char, 2
>> chars, 3 chars and 4 chars repentance, 5 chars or
>> more repeatable sequence are common? And if common, the largest common
>> chars repentance contains how many different chars?
>> 1 char repentance: AAAAAAAA...
>> 2 char repentance: ACACACACACACACA...
>>
>> Thank you.
>>
>> Weng
>>
>>  --
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