Moderator: a.zielezinski
a.zielezinski ♦ 9.3k
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Andrzej Zielezinski
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... Thank you for sharing! ...
written 5 months ago by
a.zielezinski ♦ 9.3k
3
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... You can modify your script to try downloading the sequence record three times until all fail. If all three attempts fail, skip this record.
from urllib.request import urlopen
from Bio import Entrez
import time
Entrez.email = "xxxx@xxxxx.com"
IDs = ['AY851612', 'hahdshjhdasd ...
written 5 months ago by
a.zielezinski ♦ 9.3k
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... You can use XML as query for Ensembl. The following example is for two human gene symbols (**MT-TF** and **TNRC6A**).
Format the above XML to one line and download the protein sequences using `wget`.
wget -O re ...
written 5 months ago by
a.zielezinski ♦ 9.3k
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... You can find all viral protein sequences (RefSeq) here: [https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/][1]
[1]: https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ ...
written 6 months ago by
a.zielezinski ♦ 9.3k
1
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1
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... Hi,
I highly recommend on-line service [Phylogeny.fr][1]. It performs:
- Multiple sequence alignment (Clustal / MUSCLE / T-Coffee / ProbCons)
- MSA curation (Gblock / remove positions with gaps)
- Tree construction with bootstrap (NJ / Parsimony / Maximum Likelihood / Bayes)
- Tree visualizati ...
written 7 months ago by
a.zielezinski ♦ 9.3k
4
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... Interesting question - I never thought of it that way. I ended up with something like this:
import itertools
d = {
'A': ['GCA', 'GCC', 'GCG', 'GCT'],
'C': ['TGC', 'TGT'],
'D': ['GAC', 'GAT'],
'E': ['GAA', 'GAG'],
'F': ['TTC', 'TTT'],
'G': ...
written 7 months ago by
a.zielezinski ♦ 9.3k
0
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Comment:
C: leafs in the MESH tree
... Agree, the .bin extension is misleading. ...
written 9 months ago by
a.zielezinski ♦ 9.3k
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 9 months ago by
a.zielezinski ♦ 9.3k
3
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1
answer
627
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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 9 months ago by
a.zielezinski ♦ 9.3k
2
votes
1
answer
957
views
1
answers
... Try to install libiconv package by typing `conda install -c conda-forge libiconv` ...
written 9 months ago by
a.zielezinski ♦ 9.3k
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