All Questions
Tagged with bioinformatics strings
5 questions
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optimal lifted phylogenetic alignment - how to improve time complexity?
optimal lifted alignment - is a dynamic programming algorithm. Its input is a tree $T$ with $k$ strings assigned to its leaf nodes (their length is $n$).
The algorithm then assigns strings to the ...
- 369
0
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center star alignment induces optimal alignments on pairs with the center string?
I'm trying to follow the center star algorithm error analysis - section 6.5.3. They claim that for the center string $S_1$ the distance induced by the algorithm $d(1, j)$ is always equal the optimal ...
- 369
2
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1
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How is n-gram different from k-mer?
How is n-gram different from k-mer? Both seem to be (n or k) length substrings of a larger string. Are these just terms common with different practitioners? viz. Computer Scientists and ...
- 123
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Are there any algorithms or researches on finding local alignments in partially ordered sequences?
The question is a bit unclear, so let me explain. Finding local alignments in sequences like protein sequence is a well studied area in bioinformatics, and I do not think there is any lack of ...
- 101
3
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A framework to capture common variation of sequence alignments
The global alignment problem can be generalized by setting the cost of some boundary gaps to 0.
Gaps at both end in both strings have 0 cost, then we get the semiglobal alignment.
Gaps are at the ...
- 3,103