User: Markus

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Markus310
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1 year, 7 months ago
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4 years, 12 months ago
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M****************@ruhr-uni-bochum.de

Posts by Markus

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Gene name to PDB id using Biopython
... Have you had a look at the Biopython Tutorial and Cookbook? ...
written 20 months ago by Markus310
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Comment: C: Searching for a sequence within another sequence Biopython
... I mean 'special' in contrast to general, we have a well defined use case: it's a local alignment and both sequences are clearly different in size. Because it's a local alignment, there will be no gaps in the 'unmatched' regions, so you don't need to take care of them (e.g. subtract the number of gap ...
written 20 months ago by Markus310
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Comment: C: Searching for a sequence within another sequence Biopython
... I just want to add that with the next release of ```Biopython``` (ver. 1.74), ```format_alignment```of ```pairwise2``` will prettily print local alignments (only the aligned part) with start positions (in 1-based notation). ...
written 20 months ago by Markus310
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Comment: C: Searching for a sequence within another sequence Biopython
... I think the lower part (finding the actual start position within the plasmid sequence) is a little bit too complicated in this special case. ```pairwise2```returns the aligned sequences, the score, and the begin and end values, which are the Python indices for the aligned part of the aligned sequenc ...
written 20 months ago by Markus310
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Answer: A: Biopython pairwise 2 - can I make it score an existing alignment?
... No you can't do this with Biopython's ```pairwise2```. The ```score_only``` parameter will still cause ```pairwise2.align``` to calculate an alignment from two sequences, it will just not return the alignment but only the maximium score (that it has calculated). I have written a small function whic ...
written 21 months ago by Markus310
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Answer: A: Different alignment results between Emboss Needle and Biopython pairwise2
... Sorry for the late answer, I didn't see this before. I would recommend to send such things to Biopython's Github site. The standard in EMBOSS' Needle is not to penalize end gaps (END GAP PENALTY: FALSE). This means: Gaps at the beginning and the end of the alignment are 'for free'. You must do the ...
written 21 months ago by Markus310
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Answer: A: Derive Consensus Read from pairwise2 alignment
... You need to iterate through both aligned sequences (given in ```alignments[0][0]``` and ```alignments[0][1]```) and compare both letters. E.g. like this: from Bio import pairwise2 as pw alignments = pw.align.globalxx('ACCGT', 'ACG') consensus = [] for a, b in zip(ali ...
written 3.3 years ago by Markus310
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Answer: A: Using pairwise2 for list[str] alignment
... Sorry, I saw this post quite late. There was a bug in recent Biopython versions (1.68/1.69) which prevented proper handling of list input in ```pairwise2```. This is now solved (Biopython version 1.70): from Bio import pairwise2 as pw list1 = ["MEEP", "QS", "DPSV", "EPPLS"] list2 = ...
written 3.3 years ago by Markus310
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Answer: A: how to align lists of words using biopython pairwise2
... You can do this with Biopython's ```pairwise2``` (again). There was a bug in ```pairwise2``` in Biopython releases 1.68/1.69 which prevented the proper handling of lists as input. If you run the same code in Biopython 1.70 you get the following (and expected) result: ['orange', 'pear', 'apple', ...
written 3.3 years ago by Markus310
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Comment: C: How to display mismatched sequences from alignment when using Biopython
... Have a look in Biopython's [API][1]. ```pairwise2``` is complex and allows many options. To get the same results as in EMBOSS' WATER you should use the same parameters, e.g. using ```align.localds(seq1, seq2, matrix, gap-open-penalty, gap-extend-penalty)```. In the API is an example how to implement ...
written 3.3 years ago by Markus310

Latest awards to Markus

Scholar 4.2 years ago, created an answer that has been accepted. For A: Problem with downloading CDS sequences using Biopython
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Locating a sequence in multiple fasta files
Scholar 4.3 years ago, created an answer that has been accepted. For A: Problem with downloading CDS sequences using Biopython
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Locating a sequence in multiple fasta files
Scholar 4.4 years ago, created an answer that has been accepted. For A: Problem with downloading CDS sequences using Biopython
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Locating a sequence in multiple fasta files
Scholar 4.6 years ago, created an answer that has been accepted. For A: Problem with downloading CDS sequences using Biopython

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