Sequence Alignment

[Satya Swarup Samal]

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

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Best Regards
Satya S. Samal

[Hema latha]

Dear Satya,

All these scores do have to be calculated using substitution matrices like PAM and BLOSUM.

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[gaurav kumar]

after few days i will tell you how 2 calculate score, but tell me that are u able 2 draw matrix and gap penalty or not

gaurav kumar

[Amala Santhanam]

we are using PAM and BLOSUM matrices to calculate the score

[Satya Swarup Samal]

Hello 

Hema latha and Amala Santhanam,

I am considering nucleotide sequences, So PAM and BLOSUM matrix wont help me

2009/11/12 Amala Santhanam <amala.s...@gmail.com>

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[Pradeep Shashi]

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

[jyoti gupta]

hiii,

 

satya swarup as per last mail discussion i m sending you some attached  files by these files you can find the details used in sequence alignment.

 

feel free to ask any further query.

 

thanks 

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Regards,

Jyoti Rusia Gupta



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[anamika sinha]

hiiii

 ya there r mathematical formulas tht r behind the scoring,they r achieved through corelation and regression methods and after tht determinants and matrices are involved

[Satya Swarup Samal]

Hi Anamika,

Do you have some idea how they done, some tutorial ?

2009/12/5 anamika sinha <anun...@gmail.com>

--
Best,
Satya S. Samal