hi..
U juss try out with the local and global alignment ... dis is donewith
scoring by back tracking method...
by taking2 sequences in Xn Y axis .... with d score value default u use..
fa ex: match=+2
missmatch=-2
Gap= -1
fa matchtaked diagonal value+2 and fa miss match=highest of 3 box-2
On 11/17/09, Satya Swarup Samal <[email protected]> wrote:
>
> Hello
> Hema latha and Amala Santhanam,
>
>
> I am considering nucleotide sequences, So PAM and BLOSUM matrix wont help
> me
>
> 2009/11/12 Amala Santhanam <[email protected]>
>
> we are using PAM and BLOSUM matrices to calculate the score
>>
>>
>> On 11/10/09, Satya Swarup Samal <[email protected]> wrote:
>>>
>>> Dear all,
>>>
>>> In sequence alignment algorithms e.g. Smith waterman or Needleman wunch,
>>> we have match, mismatch and gap score while comparing two sequences. But how
>>> we calculate these scores ? Is there any mathematical way or its just based
>>> on trial and error ?
>>>
>>> Thanx in advance
>>>
>>> --
>>> Best Regards
>>> Satya S. Samal
>>>
>>> --
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>
>
>
> --
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> Satya S. Samal
>
>
>
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