清空筛选条件
清空筛选条件

Sequence Distance

3 次查看（过去 30 天）
Talha
Talha 2011-7-20
I am sort of confused on how matlab gets its answers for various distance methods. My boss wants to know how matlab arrives at various answers.
I set up matlab to give me answers in fractions, so when I analyze two sequences of the same length, it gives me the denominator of the fraction to be length of the sequences (for example, if both amino acid sequences have a length of 327 then the answer has a denominator of 327). I understood this until when I analyzed two amino acid sequences with each having a different length, one being 369 amino acids long, and another being 379 amino acids long. It gave me the answer: 209/398. I don't understand how it got to having a denominator of 398 (I specifically asked it to use p-distance). When I type in "help seqpdist", it does not give me very clear explanation on how the p-distance works.
So can some one please help me out? I would greatly appreciate it!

请先登录，再回答此问题。

回答（1 个）

Lucio Cetto
Lucio Cetto 2011-7-20
When you are comparing sequences it is common to first align them using a dynamic programing algorithm. SEQPDIST uses NWALIGN to pair-wise align all possible pairs of sequences and then takes the measure from the alignment.
Consider:
seqpdist({'AACGT','AAGT','AAT'},'alpha','nt','square',1,'method','p-dist')
The alignment between 1 and 2 is 'AACGT' and 'AA-GT' =>1/5
The alignment between 1 and 3 is 'AACGT' and 'AA--T' =>2/5
The alignment between 1 and 3 is 'AAGT' and 'AA-T' =>1/4
HTH

类别

在 Help Center 和 File Exchange 中查找有关 Data Import and Export 的更多信息

标签

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by