Admin: István Albert

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István Albert ♦♦ 310
Reputation:
310
Status:
Trusted
Location:
University Park
Website:
http://www.personal.ps...
Twitter:
zumm
Last seen:
6 years, 3 months ago
Joined:
11 years ago
Email:
3@lvh.me

Current position: Research Associate Professor of Bioinformatics at Penn State

Posts by István Albert

<prev • 24 results • page 1 of 3 • next >
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Answer: A: Fast Interval Intersection Methodologies
... This code example generates 10,000 intervals then queries them for overlapping regions. Requires only the presence of Python. The code below requires the either the installation of the bx python package or alternatively you may just download the quicksect.py module and place it next to the script i ...
written 10.6 years ago by István Albert ♦♦ 310 • updated 10.6 years ago by Jane ♦♦ 0
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Answer: A: Agile Programming For Bioinformaticians - Any Suggestions?
... I think the approach is unsuited for individuals who are not comfortable with programming in general. There is a long way to go until someone becomes confident in their abilities. Before that this approach is not only ineffective, it might be even be detrimental. Instead what helps most is transpar ...
written 10.6 years ago by István Albert ♦♦ 310 • updated 10.6 years ago by Jane ♦♦ 0
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Answer: A: How To Organize A Pipeline Of Small Scripts Together?
... I don't have personal experience with this package but it is something that I plan to explore in the near future: Ruffus a lightweight python module to run computational pipelines. ...
written 10.7 years ago by István Albert ♦♦ 310 • updated 10.7 years ago by Jane ♦♦ 0
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Answer: A: Using Hdf5 To Store Bio-Data
... In the GeneTrack software we have used HDF to store values for each genomic base. Its main advantage over other storage systems was that it was able to return consecutive values with minimal overhead. For example it is extremely fast (ms) in retrieving say 100,000 consecutive values starting with ...
written 10.7 years ago by István Albert ♦♦ 310 • updated 10.7 years ago by Jane ♦♦ 0
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Answer: A: What Is The Best Way To Share Scripts Between Members Of A Lab?
... Integrating with the source code management tool is essential, that way when code gets changed everyone can easily get the updated version. Wikis are also a good idea. ...
written 10.7 years ago by István Albert ♦♦ 310 • updated 10.7 years ago by Jane ♦♦ 0
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Answer: A: How To Get The Sequence Of A Genomic Region From Ucsc?
... The Genome Browser is for visualization. To get data in many formats use the UCSC Table Browser then select the output format of your choice. You may also need to select the right group and track to get the data you want. ...
written 10.7 years ago by István Albert ♦♦ 310 • updated 10.7 years ago by Jane ♦♦ 0
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Answer: A: Turn Off Blast Search On Reverse Complement Strand In Blastn
... The -S flag can select the strands: -S Query strands to search against database (for blast[nx], and tblastx) 3 is both, 1 is top, 2 is bottom [Integer] ...
written 10.7 years ago by István Albert ♦♦ 310 • updated 10.7 years ago by Jane ♦♦ 0
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Answer: A: Where Can I Get The Secondary Structure Of A Protein?
... Protein structure prediction is a complex issue that is likely to require multiple approaches. There are many methods/tools listed at the Expert Protein Analysis System website ...
written 10.7 years ago by István Albert ♦♦ 310 • updated 10.7 years ago by Jane ♦♦ 0
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Answer: A: What Is Your Experience With The String (Interactions) Database?
... I have not used STRING in particular but I have worked with protein interactions before (DIP dataset). I recall that even experimentally produced protein-protein interactions may have very large false positive ratios (as for false negatives, who knows?) Some papers claim that up to 50% of the inter ...
written 10.7 years ago by István Albert ♦♦ 310 • updated 10.7 years ago by Jane ♦♦ 0
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Answer: A: How Much Do You Trust Geneontology?
... The GO terms and classifications are primarily an based on opinions and a human interpretation of a small group of people of what the current state of the knowledge is.Thus are more subjective than say experimental measurements would be. In fact it is surprising that it works at all; and it does ...
written 10.7 years ago by István Albert ♦♦ 310 • updated 10.7 years ago by Jane ♦♦ 0

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