Moderator: a.zielezinski
a.zielezinski ♦ 8.4k
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Andrzej Zielezinski
Posts by a.zielezinski
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... Thanks. You've saved my day. ...
written 6 weeks ago by
a.zielezinski ♦ 8.4k
3
votes
2
answers
207
views
2
answers
... 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 8 weeks ago by
a.zielezinski ♦ 8.4k
2
votes
1
answer
195
views
1
answers
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 8 weeks ago by
a.zielezinski ♦ 8.4k
3
votes
0
answers
116
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0
answers
... 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 9 weeks ago by
a.zielezinski ♦ 8.4k
0
votes
2
answers
607
views
2
answers
... Thank you very much. This feature is very helpful. I'm already showing FlexiDot to my students. ...
written 11 weeks ago by
a.zielezinski ♦ 8.4k
0
votes
2
answers
607
views
2
answers
... Wow! That's great news. I'm looking forward to it. My best wishes to the entire FlexiDot team. ...
written 3 months ago by
a.zielezinski ♦ 8.4k
1
vote
2
answers
607
views
2
answers
... It would be great to have an option to display dotplots according to cartesian coordinate system (i.e., Y axis from bottom to top, rather than from top to bottom). ...
written 3 months ago by
a.zielezinski ♦ 8.4k
0
votes
2
answers
607
views
2
answers
... IMO, the best software for creating dotplots. ...
written 3 months ago by
a.zielezinski ♦ 8.4k
1
vote
0
answers
148
views
0
answers
Comment:
C: K-mer analysis meaning
... Very clearly written and understandable [blog post about k-mers][1].
[1]: http://ivory.idyll.org/blog/2017-something-about-kmers.html ...
written 4 months ago by
a.zielezinski ♦ 8.4k
1
vote
0
answers
181
views
0
answers
... Bitscore in sequence alignment is calculated based on substitution scoring matrix. In BLASTp, the default matrix is [BLOSUM62][1]. You can see that different amino acid matches have different scores - for example, bitscore for the `W-W` match is `11` and bitscore for `G-G` is `6`. That's way, it is ...
written 5 months ago by
a.zielezinski ♦ 8.4k
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