Moderator: a.zielezinski

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a.zielezinski8.9k
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Andrzej Zielezinski

Posts by a.zielezinski

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Comment: C: Append only sequence itself to list, no metadata
... Replace `total.append(record.seq)` with `total.append(str(record.seq))`. ...
written 2 days ago by a.zielezinski8.9k
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Comment: C: Python- Searching codons using for/if
... Replace `codon==['ATG']` with `codon=='ATG'`. ...
written 26 days ago by a.zielezinski8.9k
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ETE3: error while parsing Newick tree
... Any idea why ETE Toolkit (ete3) throws an error while parsing the following Newick tree: > ((((A,B),C),(((D,E),F),(((((G,H),I),J),K),L)))(M,N)); from ete3 import Tree s = '((((A,B),C),(((D,E),F),(((((G,H),I),J),K),L)))(M,N));' t = Tree(s) The error message: ete3.parser.newick. ...
ete3 newick tree ete written 5 weeks ago by a.zielezinski8.9k • updated 5 weeks ago by Mensur Dlakic2.5k
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Comment: C: BLOSUM62 in Python
... You can then transform this dictionary into a list or NumPy's array. ...
written 6 weeks ago by a.zielezinski8.9k
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Answer: A: BLOSUM62 in Python
... blosum62 = { ('W', 'F'): 1, ('L', 'R'): -2, ('S', 'P'): -1, ('V', 'T'): 0, ('Q', 'Q'): 5, ('N', 'A'): -2, ('Z', 'Y'): -2, ('W', 'R'): -3, ('Q', 'A'): -1, ('S', 'D'): 0, ('H', 'H'): 8, ('S', 'H'): -1, ('H', 'D'): -1, ('L', 'N'): -3, ('W', 'A'): -3, ('Y', 'M'): -1, ...
written 6 weeks ago by a.zielezinski8.9k
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Answer: A: Local and global alignment combined
... As [@kuckunniwid][1] commented, you are looking for **semi-global alignment** (a.k.a **glocal**). I recommend the [needle][2] tool from EMBOSS package. By default, needle performs semi-global alignment (i.e., end gap penalties are disabled). You can play with the tool on-line or install it locally ...
written 9 weeks ago by a.zielezinski8.9k
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Comment: C: Local and global alignment combined
... Also look at this post: [Could someone suggest a fast and efficient implementation of a glocal (semi-global) sequence aligner?][1] [1]: https://www.biostars.org/p/256994/ ...
written 9 weeks ago by a.zielezinski8.9k
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Comment: C: Postdoc in computational and experimental annotation of tRNA-related sequences
... Thanks, Medhat! :-) ...
written 12 weeks ago by a.zielezinski8.9k
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Job: Postdoc in computational and experimental annotation of tRNA-related sequences
... Postdoc in computational and experimental annotation of tRNA-related sequences We are looking for a motivated postdoctoral scientist to join our team at the Department of Computational Biology (http://combio.pl), Adam Mickiewicz University in Poznan, Poland. The position is available for minimum 2 ...
genomics job trna qpcr plant hybridization written 12 weeks ago by a.zielezinski8.9k
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Answer: A: How to retrieve protein sequence data for humano in UniProt?
... Yes, you can easily download all human protein sequences. 1. Go to UniProt homepage. 2. Limit the search to human proteins by typing in the search box `organism:"Homo sapiens (Human) [9606]"`. 3. Download the FASTA sequences (Download button). ...
written 3 months ago by a.zielezinski8.9k

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Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
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Commentator 3 months ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Appreciated 4 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 6 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Appreciated 7 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Great Question 9 months ago, created a question with more than 5,000 views. For What Is The Lowest E-Value In Blast When Ncbi Rounds It Down To 0 (Zero)?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Appreciated 13 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
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