Moderator: a.zielezinski
a.zielezinski ♦ 8.7k
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Andrzej Zielezinski
Posts by a.zielezinski
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Comment:
C: NCBI expect value
... Agree! See also: [What Is The Lowest E-Value In Blast When Ncbi Rounds It Down To 0 (Zero)][1]
[1]: https://www.biostars.org/p/43484/ ...
written 27 days ago by
a.zielezinski ♦ 8.7k
0
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1
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160
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... What about this one:
blastn -task blastn -db db.fna -num_descriptions 20000 -num_alignments 20000 -outfmt 6 -query query.fna > blast.out ...
written 4 weeks ago by
a.zielezinski ♦ 8.7k
0
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1
answer
160
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1
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... try:
blastn -task blastn -db db.fna -max_target_seqs 1000000 -outfmt 6 -query query.fna > blast.out ...
written 4 weeks ago by
a.zielezinski ♦ 8.7k
0
votes
1
answer
213
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1
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Comment:
C: ORF reading in Python
... Don't forget to accept and upvote the answers which were helpful to you :) ...
written 5 weeks ago by
a.zielezinski ♦ 8.7k
0
votes
1
answer
213
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1
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Comment:
C: ORF reading in Python
... Glad it helped. Does this answer your question? ...
written 5 weeks ago by
a.zielezinski ♦ 8.7k
0
votes
1
answer
213
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1
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Comment:
C: ORF reading in Python
... Please see my answer. ...
written 5 weeks ago by
a.zielezinski ♦ 8.7k
3
votes
1
answer
213
views
1
answers
Answer:
A: ORF reading in Python
... I edited your `startstop_codon()` function to handle multiple ORFs in a single DNA sequence.
def startstop_codon(dna, frame):
dna = dna.upper()
for i in range(frame, len(dna), 3):
codon1 = dna[i:i+3]
if codon1 == 'ATG':
position1 = i
...
written 5 weeks ago by
a.zielezinski ♦ 8.7k
1
vote
1
answer
213
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1
answers
Comment:
C: ORF reading in Python
... The problem is with `position1 = dna.index(codon1)` and `position2 = dna.index(codon2)`. If the same codon is present more than once in `dna`, index() method always returns its smallest/first position. That is why, you get the same ORF length all the time. You can fix this by assigning `position1 = ...
written 5 weeks ago by
a.zielezinski ♦ 8.7k
0
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134
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... Go to PubMed and play with your query first. I suggest something like these:
- (infantile colic[mesh] AND effectiveness) AND (drugs OR herbal* OR
sugar* OR safety)
- (infantile colic[mesh] AND treatment) AND
(effectiveness OR drugs OR herbal* OR sugar* OR safety)
Remember, that parenthesi ...
written 5 weeks ago by
a.zielezinski ♦ 8.7k
1
vote
2
answers
124
views
2
answers
... [Jellyfish][1] is a popular tool for counting kmers in a multi-fasta file.
[1]: https://github.com/gmarcais/Jellyfish ...
written 6 weeks ago by
a.zielezinski ♦ 8.7k
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