I am implementing an algorithm in Python using Biopython. I have several alignments (sets of sequences of equal length) stored in FASTA files. Each alignment contains between 500 and 30000 seqs an...

Let's say you have a DNA sequence like this : AATCRVTAA where R and V are ambiguous values of DNA nucleotides, where R represents either A or G and V represents A, C or G. Is there a Biopython...

I am experimenting some problems using the Bio.Restrictions methods, I am not sure if it is due to python, biopython or my poor understanding of python. When I try to crate a RestrictionBatch foll...

I ran into this problem today, and wanted to bring it up to see if anyone else has seen it. Searching Google/SO/Biostars didn't get me anywhere. I'm running a simple restriction analysis (on a ra...

I currently have the following code which queries pubmed: from Bio import Entrez Entrez.email = "[email protected]" # Always tell NCBI who you are handle = Entrez.esearch(db="pubmed", term="...

I have a FASTA file that can easily be parsed by SeqIO.parse. I am interested in extracting sequence ID's and sequence lengths. I used these lines to do it, but I feel it's waaaay too heavy (two i...

I have a 15-mer nucleotide motif that uses degenerate nucleotide sequences. Example: ATNTTRTCNGGHGCN. I would search a set of sequences for the occurrence of this motif. However, my other sequence...

I'm trying to implement the Smith-Waterman algorithm for local sequence alignment using the affine gap penalty function. I think I understand how to initiate and compute the matrices required for c...

Hi I am currently involved in making a website aimed at combining all papillomavirus information in a single place. As part of the effort we are curating all known files on public servers (e.g. gen...

Ok so I need to extract part of a sequence from a FASTA file, using python (biopython, http://biopython.org/DIST/docs/tutorial/Tutorial.html) I need to get the first 10 bases from each sequence a...

I am trying to download some xml from Pubmed - no problems there, Biopython is great. The problem is that I do not really know how to manipulate the output. I want to put most of the parsed xml int...

I have encountered an error which I am not able to resolve. I am trying to perform the easiest set of commands that will perform a tBLASTn algorithm, looking for a sequence (sequence specified as ...

In the Biopython installation instructions, it says that if Biopython doesn't work I'm supposed to do this: export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopython' I tried doing that...

I try to score the already-aligned sequences. Let say seq1 = 'PAVKDLGAEG-ASDKGT--SHVVY----------TI-QLASTFE' seq2 = 'PAVEDLGATG-ANDKGT--LYNIYARNTEGHPRSTV-QLGSTFE' with given parameters substitut...

I trying to build a tree with BioPython, Phylo module. What I've done so far is this image: each name has a four digit number followed by - and a number: this number refer to the number of times ...