User: stacy734

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stacy73430
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Posts by stacy734

<prev • 18 results • page 1 of 2 • next >
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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 3 days ago by stacy73430
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Advice on Blast output
... 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 ...
format unix blast written 3 days ago by stacy73430
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Comment: A: Proper sed format to remove and of line characters?
... Thanks finswimmer. Sadly, that didn't seem to solve the problem. ...
written 11 weeks ago by stacy73430
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Proper sed format to remove and of line characters?
... 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+$ ...
fasta sed written 11 weeks ago by stacy73430 • updated 11 weeks ago by jcabraham0
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Answer: A: Probability of sequence with mismatches
... Hi Alex Thank you for the very clear explanation, and for taking the time! Stacy ...
written 8 months ago by stacy73430
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Probability of sequence with mismatches
... 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 ...
probability mismatches written 8 months ago by stacy73430
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Comment: A: Binning fasta sequences by size?
... Thanks to you both! ...
written 13 months ago by stacy73430
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Binning fasta sequences by size?
... 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 ...
fasta binning size written 13 months ago by stacy73430 • updated 13 months ago by Matt Shirley8.8k
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Comment: A: Exporting fasta from SQL
... Thank you very much! ...
written 18 months ago by stacy73430
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Exporting fasta from SQL
... 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. ...
fasta format sql written 18 months ago by stacy73430

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