I am using Bio.Align to do a pairwise alignment between two sequences. I want to know the pairwise alignment percent identity and pairwise alignment percent …

Hi everyone, I'm reaching out for some clarity on the ConClave scoring method as described in Philip Clausen's work (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2336-6). While I understand the general …

How lambda parameter works in BLAST? It is calculated using the following equation (https://doi.org/10.1073/pnas.87.6.2264): ![enter image description here][1] Scoring matrix is calculated using: ![enter image …

Can someone help me with this question ? For exercise 1 use pen and paper. Consider the following multiple sequence alignment from a set of …

Dear Biostars Leaders, I am a bioinformatician in our lab and I have received raw data(bcl files) on ~300 single cells RNA-Seq samples from a …

The transition probability matrix over time t is computed as P(t) = e ^Qt. In order to calculate a general set of transition probability matrices …

I am working with Scoring matrices and its evaluation. Its very important to understand the concept of entropy values and how it is derived. I …

Trying to understand substitution matrices. It seems like it is a scoring scheme for alignments, particularly if you are looking for homology? I am trying …

Here is a beginner's introduction to bioinformatics file type formats. There are a ton of different file types out there which can be overwhelming for …

<p>Following on my <a href="http://biostar.stackexchange.com/questions/4666/finding-protein-homology">previous question</a> regarding discovering protein homology. After finding sequences of interest against a profile of a family, I want to determine …