Moderator: a.zielezinski
a.zielezinski ♦ 8.6k
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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.zielezinski ♦ 8.6k
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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.zielezinski ♦ 8.6k
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... 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.zielezinski ♦ 8.6k
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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.zielezinski ♦ 8.6k
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Comment:
C: tools for finding paralogues
... What organisms do you work on? ...
written 4 months ago by
a.zielezinski ♦ 8.6k
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... Thanks. You've saved my day. ...
written 7 months ago by
a.zielezinski ♦ 8.6k
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... 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.zielezinski ♦ 8.6k
2
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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.zielezinski ♦ 8.6k
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... 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.zielezinski ♦ 8.6k
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855
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... Thank you very much. This feature is very helpful. I'm already showing FlexiDot to my students. ...
written 8 months ago by
a.zielezinski ♦ 8.6k
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