User: matt.chambers42

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Posts by matt.chambers42

<prev • 15 results • page 2 of 2 • next >
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Answer: A: Multiple (variable length) string searching in large text (e.g. Aho-Corasick)?
... If I trust all the amino acids in my peptides, I can create a trusted band that is as long as my shortest peptide? Then I could split the dataset in half for short peptides (6 AAs trusted) and long peptides (about 15 AAs trusted). Unfortunately the nucleotide restriction seems hard-coded. How hard w ...
written 3.1 years ago by matt.chambers4210
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Multiple (variable length) string searching in large text (e.g. Aho-Corasick)?
... PDict restricts the strings to constant length, and possibly also to nucleotides. I'd like to use it (or something similar) for matching peptides to proteins. But I'd like to relax the length restriction, rather than needing 1 PDict for each peptide length. What kind of performance improvement does ...
biostrings written 3.1 years ago by matt.chambers4210
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Pull request for customProDB package
... https://github.com/Bioconductor-mirror/customProDB/pull/1/files I made a simple edit on GitHub. This change is needed because the CustomProDB documentation regarding dbSNP versions is out of date (currently available versions for hg19 are snp138 through 146). ...
customprodb featurerequest written 3.3 years ago by matt.chambers4210 • updated 3.3 years ago by Dan Tenenbaum8.2k
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Comment: C: rtracklayer's browserSession hangs indefinitely
... It appears to be related to the AWS region. The same AMI in a different region (us-east-1) works fine, while us-west-2 hangs. ...
written 3.3 years ago by matt.chambers4210
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rtracklayer's browserSession hangs indefinitely
... I have isolated this hang in my R code to rtracklayer. I see it on my Amazon Linux (AWS) box but not a local server. The AWS box usually, but not always, hangs on either the browserSession() call or the genome(session) call. Here is the strace output of the AWS box: > library(rtracklayer) ...
rtracklayer written 3.3 years ago by matt.chambers4210

Latest awards to matt.chambers42

Popular Question 2.2 years ago, created a question with more than 1,000 views. For makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
Scholar 3.3 years ago, created an answer that has been accepted. For A: Multiple (variable length) string searching in large text (e.g. Aho-Corasick)?

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