User: Fucitol

gravatar for Fucitol
Fucitol100
Reputation:
100
Status:
New User
Location:
Netherlands
Website:
http://www.nbic.nl/sup...
Last seen:
7 years, 2 months ago
Joined:
7 years, 9 months ago
Email:
m***************@nbic.nl

Posts by Fucitol

<prev • 7 results • page 1 of 1 • next >
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R: Cluster Similarity Percentages With Inverted Y-Axis (Example Included)
... Hi All, Although not really a bioinformatics question (only it's purpose in phylogenetics), I was wondering how I could perform a Bray Curtis similarity clustering in R in which I show the similarity percentages on an inverted Y-axis and all tree nodes ending at 100% as shown in the following pictu ...
R clustering distance written 7.6 years ago by Fucitol100 • updated 6.5 years ago by Joseph Hughes2.7k
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Getting Exact Number Of Genomic Copies For A Specific Sequence
... Hi all, I'm trying to retrieve a set of sequences that can be used for primer design. These sequences have some requirements, e.g. present in 4 different species, not present in a number of species on a blacklist, at least 200bp in length and preferably 50 or more copies of the sequence in all spec ...
blast primer written 7.7 years ago by Fucitol100 • updated 7.7 years ago by Fabian Bull1.3k
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Comment: C: Generating A Tree From Nucleotide Frequencies
... If you're familiar with R, you can easily calculate distances between sequences using the 'dist.dna' function from the 'ape' package (http://www.oga-lab.net/RGM2/func.php?rd_id=ape:dist.dna). From there on it's easy to create a graphical tree using other functions from that package. Please let us k ...
written 7.8 years ago by Fucitol100
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Comment: C: Find Repeats In A Sequence
... You are correct Neil, that's the risk of having a Python session already open with some sequence data loaded. For safety, you can also use: sequence.upper().count(...) which works on both lower and uppercase data. ...
written 7.8 years ago by Fucitol100
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Comment: C: Genetic Distribution Of Snp Along Chromosomes - How To Get A Graphical Output?
... I'm also interested in knowing how to do something similar. I'd like to be able to create a set of chromosomes (using arbitrary lengths (non human organism)) and visualize a set of markers on them given their position. ...
written 7.8 years ago by Fucitol100
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Comment: C: Blastn - Program Runs Indefinitely When Generating Xml Formatted Output
... Using the XML format usually generates a lot of data, how many sequences are your running against which database? Like Michael asked, please show us the parameters you've used. ...
written 7.8 years ago by Fucitol100
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Answer: A: Find Repeats In A Sequence
... It's very easy to do in python using the count function: from itertools import product [sequence.count(''.join(codon)) for codon in product('ATCG', repeat=3)] Or get the results in a dictionary (you can figure out how to get the max etc yourself): dict(("".join(codon), sequence.upper().count('' ...
written 7.8 years ago by Fucitol100

Latest awards to Fucitol

Student 7.7 years ago, asked a question with at least 3 up-votes. For Getting Exact Number Of Genomic Copies For A Specific Sequence
Appreciated 7.8 years ago, created a post with more than 5 votes. For A: Find Repeats In A Sequence
Good Answer 7.8 years ago, created an answer that was upvoted at least 5 times. For A: Find Repeats In A Sequence
Teacher 7.8 years ago, created an answer with at least 3 up-votes. For A: Find Repeats In A Sequence

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