User: Perry

gravatar for Perry
Perry290
Reputation:
290
Status:
New User
Location:
philadelphia
Website:
http://hostpathogen.bl...
Last seen:
8 years, 1 month ago
Joined:
9 years, 9 months ago
Email:
e******@mail.med.upenn.edu

genomics & computational biology student @ Upenn

Posts by Perry

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Top/Bottom Confusion For Illumina Snp Calls
... Thanks. It seems to me that this naming convention conflicts with what is presented in ILLUMINA.ILLUMINA_Human_1M.xml. In the naming convention file, rs536477 is A/G and TOP. However, the rs536477 entries in the XML file are A/G and strand='bottom'. Does strand have a different meaning in the XML fi ...
written 9.2 years ago by Perry290
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Top/Bottom Confusion For Illumina Snp Calls
... Here is the problem: Illumina calls their SNPs AA,AB,BB. The meaning of A and B depend on what they call "top" or "bottom" strand. One of the problems that I am facing is that I don't have the original data. All I have is the Illumina SNP processed file with the SNP number and genotype call (AA, AB, ...
illumina dbsnp written 9.2 years ago by Perry290 • updated 9.2 years ago by Jan Oosting870
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Answer: A: Sequence Based Protein Interaction Information
... You might want to check out this cautionary paper, which claims simple sequence-based features contain insufficient information to be useful for predicting protein-protein interactions, but that protein domain-based features have some predictive value. ...
written 9.3 years ago by Perry290
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Bioconductor Quantsmooth Sex Chromosome Error
... I'm using quantsmooth to draw chromosome ideograms, but the sex chromosomes are not correctly implemented. According to the documentation, I can use 98 as X and 99 as Y, but this code is not supported by prepareGenomePlot, which translates chromosome locations to plot coordinates. prepareGenomePlot ...
bioconductor written 9.3 years ago by Perry290 • updated 9.3 years ago by Jessica0
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Conversion Between Hg18 And Hg19
... I want to draw chromosome ideogams with chromosome location data. I'm using the quantsmooth library in R, as described in this BioStar question. The quantsmooth plots are for hg18, but my data are for hg19. Is there an easy way to convert my hg19 chromosome positions to hg18 positions? I'm looking ...
conversion hg written 9.3 years ago by Perry290 • updated 9.3 years ago by Ian5.6k
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Comment: C: Post Your Prefered Bioinformatics Short Code
... If you want to learn more, check out [this post][1] on using itertools.groupby for FASTA loading. [1]: http://drj11.wordpress.com/2010/02/22/python-getting-fasta-with-itertools-groupby/ ...
written 9.7 years ago by Perry290 • updated 3 months ago by RamRS25k
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Answer: A: How Do I Match Orthologues In One Species To Another, Genome Scale?
... Try [ROUNDUP](http://roundup.hms.harvard.edu/roundup/index.php?action=input_cluster) or homologene ...
written 9.7 years ago by Perry290 • updated 3 months ago by RamRS25k
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Comment: C: Markov Chain For Generating Random Protein Sequences
... Thanks. The first link helped. ...
written 9.7 years ago by Perry290
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Markov Chain For Generating Random Protein Sequences
... I have 1000+ protein sequences. I want to generate random sequences using a Markov model based on residue transitions found my sequences. I'm told Matlab will make a Markov chain based on multiple sequences, but I would like to use a free alternative to Matlab (python, ruby, R, etc). Can anyone prov ...
sequence protein random written 9.7 years ago by Perry290 • updated 8.9 years ago by Istvan Albert ♦♦ 81k
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Answer: A: How To Organize A Pipeline Of Small Scripts Together?
... Most of my work is in python, so I use paver, which is similar to makefiles or rake for ruby, but gives you access to all python libraries. ...
written 9.8 years ago by Perry290

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