Moderator: a.zielezinski

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a.zielezinski8.7k
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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.zielezinski8.7k
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Comment: C: blastn not returning all the expected results
... 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.zielezinski8.7k
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Comment: C: blastn not returning all the expected results
... try: blastn -task blastn -db db.fna -max_target_seqs 1000000 -outfmt 6 -query query.fna > blast.out ...
written 4 weeks ago by a.zielezinski8.7k
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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.zielezinski8.7k
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Comment: C: ORF reading in Python
... Glad it helped. Does this answer your question? ...
written 5 weeks ago by a.zielezinski8.7k
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Comment: C: ORF reading in Python
... Please see my answer. ...
written 5 weeks ago by a.zielezinski8.7k
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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.zielezinski8.7k
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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.zielezinski8.7k
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Comment: C: Queries in PubMed and MEDLINE with Entrez
... 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.zielezinski8.7k
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Comment: C: Calculating dinucleotide frequencies for each sequence in a multi fasta file
... [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.zielezinski8.7k

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 5 weeks ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Appreciated 9 weeks 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 3 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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Great Question 4 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 4 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Appreciated 8 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
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
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Teacher 16 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 16 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Appreciated 16 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 16 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
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