Moderator: Pawel Szczesny

gravatar for Pawel Szczesny
Pawel Szczesny3.2k
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Bioinformatics, genomics, systems biology and teaching.

Posts by Pawel Szczesny

<prev • 161 results • page 2 of 17 • next >
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Comment: C: Exonerate ** FATAL ERROR **: Unrecognised symbol 'J' (ascii:74)
... I would not remove it, unless you require from exonerate 100% agreement (this is not recommended BTW) or mismatch codon can ruin your analysis. ...
written 5.0 years ago by Pawel Szczesny3.2k
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Answer: A: Exonerate ** FATAL ERROR **: Unrecognised symbol 'J' (ascii:74)
... J is a placeholder "used in cases where chemical or crystallographic analysis of a peptide or protein cannot conclusively determine the identity of a residue." It does not represent a proteinogenic amino acid (but an amibiguity between I and L) and exonerate does not have a translation table for it. ...
written 5.0 years ago by Pawel Szczesny3.2k
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Answer: A: How to generate .sra files from Fastq
... I have never used it but Mothur has a command "make.sra". ...
written 5.0 years ago by Pawel Szczesny3.2k
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Comment: C: Stress Response: is there a mapping between KEGG and COG? [solved]
... Cool, I didn't know about KOALA. BTW, you could add your solution as an answer and later accept it. That way the question will be marked as answered (you don't get points for answering your own question, so it's not seen as wrong behaviour) and site will be kept clean. ...
written 5.0 years ago by Pawel Szczesny3.2k
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Answer: A: Stress Response: is there a mapping between KEGG and COG?
... Given that underlying functional hierarchy is different (KOs map to GO, COGs don't), I don't think you can obtain one-to-one mapping for all identifiers (you will get one-to-many quite frequently, plus lots of missing ones). This will make any comparison with the previous research quite difficult.  ...
written 5.0 years ago by Pawel Szczesny3.2k
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Comment: C: Too late to switch to Bioinformatics?
... From my perspective, trying to join a bioinformatics department (such that develops a software) as a computer scientists has a much higher chance of success, than trying to join such a department as a biologist.  ...
written 5.0 years ago by Pawel Szczesny3.2k
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Comment: C: Too late to switch to Bioinformatics?
... You write: "bioinformatics is not about coding, it's about biology" but it seems to me that you mistake computational biology for bioinformatics. Half of the posters in this forum had never asked and answered a meaningful biological question. That doesn't make them less-scientists or something. Higg ...
written 5.0 years ago by Pawel Szczesny3.2k
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Answer: A: Too late to switch to Bioinformatics?
... You are worry about the wrong thing. Have a look at the resume of Robert Edgar and see his publication record.  Worry about building useful things, not about being too late. The party ain't over. ...
written 5.0 years ago by Pawel Szczesny3.2k
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Comment: C: Phylogenetic tree for 16S rRNA with whole taxonomy included
... Finally it worked (uff, half of the time spent looking for compatible linux version). Thanks a lot for the pointer - export went smoothly.  ...
written 5.1 years ago by Pawel Szczesny3.2k
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Comment: C: Phylogenetic tree for 16S rRNA with whole taxonomy included
... Yes, SILVA... I should probably mention that I hope I could avoid fighting with ARB software (badly written, crashes, requires weird versions of libraries). SILVA's official exports do not contain large trees.  ...
written 5.1 years ago by Pawel Szczesny3.2k

Latest awards to Pawel Szczesny

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Popular Question 4.9 years ago, created a question with more than 1,000 views. For What Is The Best Pipeline For 16S Rna Metagenome Analysis?

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