Moderator: a.zielezinski
a.zielezinski ♦ 9.1k
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Andrzej Zielezinski
Posts by a.zielezinski
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Comment:
C: leafs in the MESH tree
... Agree, the .bin extension is misleading. ...
written 4 weeks ago by
a.zielezinski ♦ 9.1k
2
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Answer:
A: leafs in the MESH tree
... MeSH trees are stored in the [ftp://nlmpubs.nlm.nih.gov/online/mesh/MESH_FILES/meshtrees/mtrees2020.bin][1] text file. However, you need to parse the file to get all the leaves.
Few lines from the `mtrees2020.bin` file:
Infections;C01
Aneurysm, Infected;C01.069
Arthritis, Infectious;C0 ...
written 4 weeks ago by
a.zielezinski ♦ 9.1k
3
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... The problem is with your `msa.phy` file. Phylip format has [certain specifications][1].
Your file should look like this:
3 253
esv1 TACGTAGGTGGCGAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAAACTTGAGTGCAGAAGAGGAAAGCGGAATTCCACGTGT ...
written 6 weeks ago by
a.zielezinski ♦ 9.1k
1
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1
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... Try to install libiconv package by typing `conda install -c conda-forge libiconv` ...
written 6 weeks ago by
a.zielezinski ♦ 9.1k
1
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1
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... Replace `total.append(record.seq)` with `total.append(str(record.seq))`. ...
written 3 months ago by
a.zielezinski ♦ 9.1k
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... Replace `codon==['ATG']` with `codon=='ATG'`. ...
written 4 months ago by
a.zielezinski ♦ 9.1k
3
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1
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... 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 4 months ago by
a.zielezinski ♦ 9.1k
• updated
4 months ago by
Mensur Dlakic • 4.2k
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Comment:
C: BLOSUM62 in Python
... You can then transform this dictionary into a list or NumPy's array. ...
written 5 months ago by
a.zielezinski ♦ 9.1k
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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 5 months ago by
a.zielezinski ♦ 9.1k
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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 6 months ago by
a.zielezinski ♦ 9.1k
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