User: ronaldnieuwenhuis

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Posts by ronaldnieuwenhuis

<prev • 11 results • page 1 of 2 • next >
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Comment: C: How to extract all non-seqenced positions from a genome (Fasta file)?
... Though this is a nice oneliner it is very slow on large files. Although I did not search for a particular fast way to do this it took that much time and such a huge amount of memory(!) that I decided to quickly write it in python. It does use Biopython though. #!/usr/bin/python3.6 imp ...
written 5 weeks ago by ronaldnieuwenhuis0
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Is the most recent Normd version (1.3) missing the executable to remove badly aligned sequences?
... I want to remove badly aligned sequences from MSAs. Very helpful were these issues on BioStars:   https://www.biostars.org/p/4855/ https://www.biostars.org/p/5798/ But in the version 1.3 of NorMD it seems the normd_rs executable is removed. Although it may still be there but not in the form t ...
alignment sequence written 3.5 years ago by ronaldnieuwenhuis0 • updated 3.4 years ago by Biostar ♦♦ 20
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Which Alphabet should I use for making a substitution matrix
... Hello, In order to make a custom substitution matrix I use clastalo to perform a msa and subsequently I use the SubsMat module trying to create a substition matrix. I have to specify an alphabet and, with the biopython Alphabet and IUPAC modules being though to understand, I haven't been able to f ...
alphabet biopython written 4.6 years ago by ronaldnieuwenhuis0 • updated 4.6 years ago by Peter5.8k
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Comment: C: How is this blastresult possible?
... Thank you for your answer! ...
written 4.7 years ago by ronaldnieuwenhuis0
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Comment: C: How is this blastresult possible?
... Thank you for your reply sir, I was clearly having a wrong idea about 'filtering' my data and I will certainly think more and better about my future plan to not oversimplify them. ...
written 4.7 years ago by ronaldnieuwenhuis0
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Comment: C: How is this blastresult possible?
... Thank you sir for your comment. The reason the question is a bit briefly because I expected it to be enough to answer, so my apologies. I cannot provide all the information you asked for. (I will modify my question tomorrow with the requested information, I cannot reach it right now)   ...
written 4.7 years ago by ronaldnieuwenhuis0
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How is this blastresult possible?
... Hello guys, I am a bioinformatics student and I am having metagenomic data (contigs) of the content of a fermentation plant. This means there is possible plant, animal and bacterial DNA material in it. I am only interested in some enzyme produced by methanogenic bacteria. So that is why I try to fi ...
megablast result written 4.7 years ago by ronaldnieuwenhuis0 • updated 4.7 years ago by Michael Dondrup46k
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Comment: C: What input does blastdb_aliastool need?
... Thank you for your time and answer sir, it worked out for me! :) The databases I created with makeblastdb were not giving an -out argument so all my databases were called <dbname>.fa.nsq and so on. So I confused meself, but the problem is solved. ...
written 4.7 years ago by ronaldnieuwenhuis0
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Comment: C: What input does blastdb_aliastool need?
... May I ask you for a little clarification of your answer. Do you mean with precompiled blast databases a directory consisting of multiple .nsq, .nin, .nhr files? Maybe you can provide me an example of how the -dblist argument has to look like? ...
written 4.7 years ago by ronaldnieuwenhuis0
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What input does blastdb_aliastool need?
... Hello, I want to use the blatdb_aliastool to aggregate multiple databases. But I am wondering if the -dblist option uses .FASTA files or .nsq files? If tool can only be used with .nsq files it means I have to use makeblastdb for all my fastafiles I guess? ...
blastdb_aliastool written 4.7 years ago by ronaldnieuwenhuis0 • updated 4.7 years ago by rtliu2.0k

Latest awards to ronaldnieuwenhuis

Popular Question 10 months ago, created a question with more than 1,000 views. For Which Alphabet should I use for making a substitution matrix
Popular Question 3.5 years ago, created a question with more than 1,000 views. For What input does blastdb_aliastool need?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How is this blastresult possible?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Why does makeblastdb raise this exception on linux?

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