User: Sequencegeek

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Sequencegeek740
Reputation:
740
Status:
New User
Location:
UCLA
Last seen:
8 years, 8 months ago
Joined:
9 years, 7 months ago
Email:
c***********@gmail.com

I do post transcriptional research at UCLA.

Posts by Sequencegeek

<prev • 38 results • page 2 of 4 • next >
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Answer: A: Is There Any Script To Count Repeats In Protein Sequences?
... The script below should work. Use the countRepeat fxn: Seq: your protein amino acid sequence minTimes: The minimum times a kmer should repeat before it is counted as a repeat- kmerLength: The length of the repeat (1,2,3,4,5,etc.) Note: this will find all repeats for all slides (kin ...
written 9.4 years ago by Sequencegeek740
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Comment: C: What'S The Best Generic Scripting Tool For Bioinformatics?
... Agreed. The trifecta of bioinformatics: Tools, shell/linux knowledge, and python/perl/other. ...
written 9.4 years ago by Sequencegeek740
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Answer: A: Quick Command To Split Large Blastx Files?
... I made this script to split files into X pieces. If your results are on a line each this should work, and if they aren't then it can be modified fairly easy. Good luck. #!/bin/bash fN=$1 outD=$2 numParts=$3 bn=`basename "$fN"` echo using basename $bn #get the number of lines in the file IFS=' ' r ...
written 9.4 years ago by Sequencegeek740 • updated 9.4 years ago by Istvan Albert ♦♦ 85k
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Comment: C: Parallel Computing With Key/Value Stores (Multiple Writes)
... @Aleksandr Levchuk: Redis looks amazing, but If I can get a solution that doesn't load all the databases into memory it would be better. I'm currently trying out both Redis and Tyrant. PS: I've referenced your example about loading 100 processes using a single database thread multiple times since ...
written 9.5 years ago by Sequencegeek740
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Comment: C: Parallel Computing With Key/Value Stores (Multiple Writes)
... @gawp Thanks for the info everyone. Will a network interface be safe with NFS? It is only using one process/server per database (Tyrant, Tycoon, Redis) so I'd venture that it would be? ...
written 9.5 years ago by Sequencegeek740
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Comment: C: Parallel Computing With Key/Value Stores (Multiple Writes)
... Thanks for the info everyone. Will a network interface be safe with NFS? It is only using one process/server per database (Tyrant, Tycoon, Redis) so I'd venture that it would be? ...
written 9.5 years ago by Sequencegeek740
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Comment: C: Parallel Computing With Key/Value Stores (Multiple Writes)
... Thanks for the reply. I can update all the writes at the same time after manipulating the data (I think/hope) using transactions. The downside is I have to store the data in ram before writing it and for some jobs that's why I need the random access. If the reason it hangs is because I do too man ...
written 9.5 years ago by Sequencegeek740
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Comment: C: Parallel Computing With Key/Value Stores (Multiple Writes)
... Code updated. Yes I'm using processes, one cpu for each process. I think it might have to do with I/O also, but I don't know how to confirm? It if was a matter of throughput wouldn't doing 100 read only processes be slow as well, because only the write processes hang. Any suggestions how to veri ...
written 9.5 years ago by Sequencegeek740
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Comment: C: Parallel Computing With Key/Value Stores (Multiple Writes)
... I'm copying the question there right now but I figured I ask here as well because people might have experience with it. ...
written 9.5 years ago by Sequencegeek740
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Parallel Computing With Key/Value Stores (Multiple Writes)
... Hi everyone, I've been setting up a data management system using Berkeley DB and the python bindings (bsddb3) to run parallel tasks for ~ 80 million RNA sequences that have properties similar to the "Target RNA" schema below. Target RNA length, sequence, expression, mismatchPositions, etc. Probl ...
database parallel written 9.5 years ago by Sequencegeek740 • updated 2.0 years ago by amirouche.boubekki10

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