Hi everyone, I am trying to compare sequences in a pairwise fashion to obtain percent similarity scores. For context, these sequences are non-coding DNA that …

Dear All, I need to align many sequences against a single reference sequence **locally**. And I need the **ungapped** alignment. I ran the bowtie2 with …

Hi there, I have amplicon data that I want to align with BWA - I set the softclipping penalty very high (`-L 50`) to force …

Is there a way to use custom matrix for nucleotide aligner in Biopython pairwise2 module? I want to decrease penalties for A->G, C->T substitutions. import …

I want to align two protein sequences. For example, <br> sequence 1: AYGEC <br> sequence 2: A(GG)C Note that sequence 2 is always shorter than …

I'm trying to calculate all-pair protein sequence similarity score via **blastp**. Later using this as a feature for my machine learning model. So that I …

I am running a BLASTN search on a 15-nucleotide sequence with the following parameters: expect threshold = 1000, word size = 7, match/mismatch = 1, …

<p>Hi all. Iam trying to calculate the alignment score of these two sequences</p> <pre><code>A_TAAG_A A_G____A </code></pre> <p>match = 1 mismatch = -1 gap opening = …

<p>Can anyone suggest how to use samtools to filter only hits where there is a insertion in the reference that splits the sequence hit roughly …

<p>Does anyone know of any general-purpose semiglobal alignment tools? Something like BLAST for semiglobal alignments instead of local alignments. </p> <p>A semiglobal alignment is like …