Tag: pairwise2

Alignment error using Biopython 1 Hello, i am trying to write a program using biopython that will align some sequences from a fasta file (for the test that i will present 5 of them) against a fasta file containing a genome. For each, gene-genome alignment i want the score of…

(This may be a really stupid question, but I cannot find what I’m looking for in the documentation) I’m trying to align multiple sequences at once. From the biopython package, I can see how I can make an alignment of two sequences, e.g.: from Bio.Seq import Seq from Bio import…

Segmentation fault Biopython pairwise alignment 0 Hi everybody ! I’m working in order to create my own pairwise sequence alignment program in Python. I use the pairwise2.align command from Bipython. When I use it with small sequences it works. I put the code bellow (2 for a match, -2 for…

I’ve been racking my brains about the best way to do this for a while now but am no closer to the answer it seems, so I could use some help! I’ll explain the problem conceptually, then in context as that may help. Essentially the problem is this: Given a…

Hi everyone, I noticed that the Bio.pairwise2 module has been deprecated, so I wanted to switch to Bio.Align.PairwiseAligner in my scripts, as suggested by the warning message. I used to do the following to calculate sequence identity and query coverage: aln1, aln2, _, start_aln, end_aln = pairwise2.align.localds(x_seq, y_seq, blosum_matrix, -11,…

There are gaps where mismatches should be in pairwise alignment (Biopython-pairwise2) 1 Hi! I’m trying to do a pairwise alignment. As I explained in my previous post, I’m trying to filter the sequences by their alignment scores or end values. However, there is one thing that I can not understand…

Setup I am reporting a problem with Biopython version, Python version, and operating system as follows: 3.6.13 | packaged by conda-forge | (default, Feb 19 2021, 05:36:01) [GCC 9.3.0] CPython Linux-5.11.0-41-generic-x86_64-with-debian-bullseye-sid 1.78 # also tested on windows-subsystem 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] CPython Linux-5.10.16.3-microsoft-standard-WSL2-x86_64-with-glibc2.31 1.78 Expected behaviour…

Find most similar peptide and calculate distance? 0 Hello! I have mutant and wild peptide. I select some short subpeptide containing mutation and i want to find the most similar subpeptide (preferably of the same length) in the wild peptide to compare its immunological properties to the mutant one. And…