User: Mrawlins

gravatar for Mrawlins
Mrawlins420
Reputation:
420
Status:
New User
Location:
Retirement
Last seen:
9 years, 10 months ago
Joined:
10 years ago
Email:
m***************@pnl.gov

I've retired from bioinformatics, pursuing other career options.

Posts by Mrawlins

<prev • 11 results • page 1 of 2 • next >
3
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Answer: A: Hash Size Vs Read Identity, Mosaik Or Other Ngs Mapping Tools
... It seems that the number associates with hs is not the size of the hash per se, but the size of nucleotide oligomer that gets put into the hash. So hs 17 will be a smaller hash of 17-bp sequences than hs 11 (11-bp sequences). The larger sequences will result in fewer random hits, but a sequence th ...
written 9.9 years ago by Mrawlins420
16
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5
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5
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Answer: A: Cuda/Gpu Processing And Bioinformatics
... Most of the difficult problems in biology are readily reduced to graph or set problems. They're hard not because these problems have difficult math but because they are on large datasets with lots of inter-dependencies. Your example of de-novo assembly is a good one. Doing assembly on 300 million ...
written 9.9 years ago by Mrawlins420
6
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8
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8
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Answer: A: Why There Are No Proteomics Questions In Biostar?
... Getting started in proteomics is hard compared to genomics. I started out in LC-MS, then LC-MS/MS and ended up in RNA-Seq for next-gen sequencers. Understanding genomic and transcriptomic studies does not require much understanding of chemistry. You need to understand cellular processes to interp ...
written 9.9 years ago by Mrawlins420
3
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6
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6
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Answer: A: Open Source Mass Spec Search Engines?
... We developed [Polygraph](http://omics.pnl.gov/software/MSPolygraph.php). It's based on the algorithm from http://pubs.acs.org/doi/abs/10.1021/jp905049d, which documents some of the preliminary results using a hybrid database/library search. A manuscript with updated results was just submitted for ...
written 9.9 years ago by Mrawlins420 • updated 13 months ago by RamRS30k
2
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2
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Answer: A: Why Is Statistical Coupling Analysis Not Confounded By Shared Evolutionary Histo
... It seems to me that covariance is a originally determined by the thermodynamics governing protein/peptide folding and those covariances are propagated through evolutionary descent. The questions being asked of SCA and evolutionary history have some overlap. SCA may pick up on features missed by evo ...
written 9.9 years ago by Mrawlins420
1
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3
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Comment: C: In Silico Genome Digestion ?
... This java program provided all the results I needed with less hassle than many of the web-based tools I had tried. Thanks! ...
written 9.9 years ago by Mrawlins420
1
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4
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Comment: C: Comparing Snps Across Populations
... Every individual counts as a single data point. The more data you have, the more reliable the results are. The sensitivity and specificity are only as accurate as 1/N at most. Assume you have a 200/N % chance of missing a useful SNP. What's the smallest N you can live with for your experiment? That' ...
written 10.0 years ago by Mrawlins420
6
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4
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7.1k
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Answer: A: Comparing Snps Across Populations
... The largest differences in SNP distribution between the two populations are ideal targets for further study. Ideally you would find a single SNP that is 100% one way in one phenotype and 100% the other way in the other phenotype. That isn't particularly likely in most cases, though. Often even fo ...
written 10.0 years ago by Mrawlins420
0
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8
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Comment: C: As A Grad Student, Who Owns My Code?
... The copyright technically belongs to the university. Most of the things you write will be of no use to them, they won't care, you do what you like and they'll never know. If you run afoul of this, though, you can get in some murky waters. If you're worried about it, you probably ought to talk to som ...
written 10.0 years ago by Mrawlins420
4
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2
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5.8k
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Answer: A: Converting A Snp Gff3 File To Vcf Format
... It looks like there is a script to do convert GFF4 to VCF at http://www.pacbiodevnet.com/ConversionTools . It may support GFF3 as well, but if not it may be faster to modify this than create one from scratch. ...
written 10.1 years ago by Mrawlins420

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