Moderator: a.zielezinski
a.zielezinski ♦ 8.9k
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Andrzej Zielezinski
Posts by a.zielezinski
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... Replace `total.append(record.seq)` with `total.append(str(record.seq))`. ...
written 2 days ago by
a.zielezinski ♦ 8.9k
0
votes
2
answers
113
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2
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... Replace `codon==['ATG']` with `codon=='ATG'`. ...
written 26 days ago by
a.zielezinski ♦ 8.9k
2
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1
answer
97
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1
answer
... 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. ...
written 5 weeks ago by
a.zielezinski ♦ 8.9k
• updated
5 weeks ago by
Mensur Dlakic • 2.5k
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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.zielezinski ♦ 8.9k
0
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1
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245
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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.zielezinski ♦ 8.9k
0
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... 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.zielezinski ♦ 8.9k
0
votes
1
answer
180
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1
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... 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.zielezinski ♦ 8.9k
0
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answers
206
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... Thanks, Medhat! :-) ...
written 12 weeks ago by
a.zielezinski ♦ 8.9k
3
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answers
206
views
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... 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 ...
written 12 weeks ago by
a.zielezinski ♦ 8.9k
2
votes
1
answer
132
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1
answers
... 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.zielezinski ♦ 8.9k
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