User: stacy734
stacy734 • 30
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Posts by stacy734
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Answer:
A: Advice on Blast output
... Thanks!
For others who may read this, the parameter in question can either be sskingdom or sblastname.
Stacy ...
written 10 weeks ago by
stacy734 • 30
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... Hi everyone,
I am running blastn on the commandline, trying different options for formatting. This command:
blastn -query blastme.fasta -out remote.blastn -db nr -evalue 1e-30 -outfmt 18 -max_target_seqs=1 &
Gives output that looks like this:
_________________________________
Accession ...
written 10 weeks ago by
stacy734 • 30
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... Thanks finswimmer.
Sadly, that didn't seem to solve the problem. ...
written 5 months ago by
stacy734 • 30
2
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240
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... Hi everyone,
I have a fasta file with some junk at the end of many lines, which I would like to remove using sed.
I have tried these formats, but am getting errors inre illegal variable names:
sed -e "s/NNG$//g"
sed -e "s/NNG\$//g"
sed -e "s/NNG$//g"
sed -e "s/NNG+$ ...
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... Hi Alex
Thank you for the very clear explanation, and for taking the time!
Stacy ...
written 10 months ago by
stacy734 • 30
2
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3
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337
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3
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... Hi all,
I'm drawing a blank as to how to calculate the probability of a sequence of length N with some number of mismatches.
For example, a specific 50-mer will occur once in 4^50 ( or 1.267 E 30).
(ignoring reverse compliments for this example for clarity.)
What would it be if one mismatch were ...
written 10 months ago by
stacy734 • 30
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Comment:
A: Binning fasta sequences by size?
... Thanks to you both! ...
written 15 months ago by
stacy734 • 30
10
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4
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616
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6 follow
4
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... Hi everyone,
I have a large fasta file and need to bin it by size: everything 200 nt and up in one file, and everything 199 or smaller in another. I have found some useful scripts that will remove the smaller sequences, but they are discarded and I need to keep them in a separate file.
Can anyone ...
written 15 months ago by
stacy734 • 30
• updated
15 months ago by
Matt Shirley ♦ 8.9k
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Comment:
A: Exporting fasta from SQL
... Thank you very much!
...
written 21 months ago by
stacy734 • 30
0
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926
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... Hi everyone,
I have sequences stored in an SQL database, with the header stored in one field and the sequence (single line) in another.
header1 GACTACGACT...
header2 ATACGATCAT...
I've been exporting sequences as a csv and running another process to put them in proper fasta format. ...
written 21 months ago by
stacy734 • 30
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