0
votes
1answer
29 views

Applying Constraint Programming to sequence alignment/analysis

My Masters program is focused on formal methods such as SAT solving and constraint programming. I am interested in applying such techniques to problems in sequence alignment and sequence analysis, ...
1
vote
1answer
37 views

How is the GenBank used in typical biological research? [closed]

How is the GenBank used in typical biological research? According to the GenBank statistics, the database contains about 100 million sequences. I find it difficult to understand why is all that data ...
1
vote
1answer
79 views

Datasets of aligned nucleotide sequences [on hold]

Where can I find some datasets of aligned nucleotide sequences? And what should I assume about the accuracy of the alignments there? (I would like to use such datasets for training the alignment ...
2
votes
1answer
45 views

Standard datasets for testing new multiple sequence alignment algorithms?

Are there any open and freely distributed standard datasets for testing new algorithms for multiple sequence alignment?
3
votes
1answer
92 views

What is the state-of-the-art algorithm for multiple sequence alignment?

Which algorithm or algorithms are considered the standard or state-of-the-art for multiple sequence alignment? How big is the need for better algorithms? How many sequences need to be alignment in a ...
4
votes
1answer
64 views

Blosum matrix with probabilities instead of the positive and negative scores

I am trying to find a version of the BLOSUM matrix that has the frequencies instead of the scaled log-odds. i.e. instead of the common version that tells us that the score LEU/ASP is -4, I would like ...
1
vote
1answer
142 views

Codon alignment via Python? [closed]

I have pairs of coding DNA sequences which I wish to perform pairwise codon alignments via Python, I have "half completed" the process. So far.. I retrive pairs of orthologous DNA sequences from ...
1
vote
2answers
81 views

what does sequences overlap indicate

what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other and how does one go on to ...