Question: Biopython tools online
gravatar for nobu.kim66
2 days ago by
nobu.kim6610 wrote:


For a school project, my group and I were thinking of making a full suite of Biopython tools available via a web interface (no coding necessary by users). Would there be any demand for this kind of website? Or would it be redundant since there is Emboss?

biopython • 91 views
ADD COMMENTlink modified 2 days ago • written 2 days ago by nobu.kim6610

I think making a tool that requires no coding but notionally provides BioPython functionally is a bit of a contradiction in terms.

To my mind the entire point of BioPython is to be able to rapidly code your own tools. It might make for a fun/informative project, but I'm not sure of its overall utility. This may just be me though.

ADD REPLYlink written 2 days ago by Joe18k

@Joe, we are starting with implementing our own Needleman and Waterman with a Plotly Dash frontend. Unfortunately, our group stumbled on Needleman so was looking at using:

6.6.2  PairwiseAligner

The new Bio.Align.PairwiseAligner implements the Needleman-Wunsch,
Smith-Waterman, Gotoh (three-state), and Waterman-Smith-Beyer global
and local pairwise alignment algorithms. We refer to Durbin et al.
[16] for in-depth information on sequence alignment algorithms.

Biopython automatically chooses the algorithm based on the gap penalty parameters but we are having trouble discerning among them:

>>> print(aligner) Pairwise sequence aligner with parameters   match_score: 1.000000   mismatch_score: 0.000000  
 target_internal_open_gap_score: 0.000000  
 target_internal_extend_gap_score: 0.000000  
 target_left_open_gap_score: 0.000000  
 target_left_extend_gap_score: 0.000000  
 target_right_open_gap_score: 0.000000  
 target_right_extend_gap_score: 0.000000  
 query_internal_open_gap_score: 0.000000  
 query_internal_extend_gap_score: 0.000000  
 query_left_open_gap_score: 0.000000  
 query_left_extend_gap_score: 0.000000  
 query_right_open_gap_score: 0.000000  
 query_right_extend_gap_score: 0.000000  
 mode: local <BLANKLINE>
ADD REPLYlink modified 1 day ago by ATpoint41k • written 2 days ago by nobu.kim6610
  1. Do not add answers unless you're answering the top-level post (which here is your original question). Use Add Comment or Add Reply instead.
  2. Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
ADD REPLYlink written 2 days ago by RamRS30k

What are internal, target, query?

ADD REPLYlink written 2 days ago by nobu.kim6610

Target and query refer to the 2 sequences. "Internal" means opening a gap within the sequence c.f. the ends of the sequence (the former is generally more expensive).

ADD REPLYlink written 2 days ago by Joe18k
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