Moderator: a.zielezinski

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a.zielezinski8.6k
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Andrzej Zielezinski

Posts by a.zielezinski

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Comment: C: outliers in XP-EHH
... The 1.5xIQR is a rule of thumb (and generally a good one, although it may not always be appropriate) by John Tukey for determining outliers. Outliers here are defined as observations that fall below `Q1 − 1.5*IQR` or above `Q3 + 1.5*IQR`, where IQR = Q3-Q1 and Q1 is first quartile and Q3 is third qu ...
written 3 days ago by a.zielezinski8.6k
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Comment: C: treating out-of-range values
... I would go with option 2 until the underlying distribution of values is symmetric. For example, replacing given parts of a sample at the high and low end with the most extreme remaining values is used while calculating the [Winsorized mean][1]. [1]: https://en.wikipedia.org/wiki/Winsorized_mean ...
written 11 days ago by a.zielezinski8.6k
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Comment: C: [BioPython] Parse blast tabular output
... Unfortunately you can't sort the blast records by query coordinate. However, you can sort it via Linux sort. For example, `sort -k 1,1 -k 7,7n blast.txt` will sort hsps by hsp.qstart. ...
written 13 days ago by a.zielezinski8.6k
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Comment: C: ClustalW multiple output files
... You can use [readseq][1] for format conversion (e.g. Nexus > Fasta). [1]: http://manpages.ubuntu.com/manpages/xenial/man1/readseq.1.html ...
written 4 months ago by a.zielezinski8.6k
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Comment: C: tools for finding paralogues
... What organisms do you work on? ...
written 4 months ago by a.zielezinski8.6k
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Comment: C: Any software to view newick/nexus trees command line?
... Thanks. You've saved my day. ...
written 7 months ago by a.zielezinski8.6k
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Answer: A: Filtering HmmScan Domain Results
... The perl script, [pfam_scan.pl][1] (from EBI) was developed for this exact purpose. `pfam_scan.pl` searches one or more sequences for matching Pfam domains using standard `hmmscan`. In addition, the program groups together families which have a common evolutionary ancestor in clans. Where there a ...
written 7 months ago by a.zielezinski8.6k
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Answer: A: I want Blast old
... You can download executables of old BLAST (in all versions) from the NCBI ftp server: [ftp://ftp.ncbi.nlm.nih.gov/blast//executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-win64.exe][1]. [1]: ftp://ftp.ncbi.nlm.nih.gov/blast//executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-win64.exe ...
written 7 months ago by a.zielezinski8.6k
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Comment: C: How to prove one set of protein is more conserved than the other set?
... Generate all-versus-all pairwise global alignments in set A and calculate mean percent identity with standard deviation. Do the same for the sequences within set B. Then, depending on the distribution of identities apply t-test or Mann-Whitney test to see whether the difference between the two sets ...
written 8 months ago by a.zielezinski8.6k
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Comment: C: FlexiDot: highly customizable, ambiguity-aware dotplots
... Thank you very much. This feature is very helpful. I'm already showing FlexiDot to my students. ...
written 8 months ago by a.zielezinski8.6k

Latest awards to a.zielezinski

Good Answer 14 days 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
Great Question 14 days 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 14 days ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Appreciated 4 months 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 6 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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
Good Answer 10 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
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 11 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 12 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Appreciated 12 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 12 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 12 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Good Answer 13 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
Scholar 13 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Appreciated 13 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 13 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Good Answer 13 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
Appreciated 13 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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