User: Mensur Dlakic

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Mensur Dlakic3.3k
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USA
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http://www.montana.edu...
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2 hours ago
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7 months, 4 weeks ago
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Posts by Mensur Dlakic

<prev • 328 results • page 1 of 33 • next >
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Comment: C: methplotlib: visualization and analysis of modified nucleotides from nanopore se
... Saw the paper couple of days ago, well done! Can't say that I am crazy about the name, even though it is problem-appropriate. ...
written 13 hours ago by Mensur Dlakic3.3k
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Answer: A: How to Detect Frameshifts in a Protein Alignment
... > I've tried calculating a rolling window of edit distances between the alignments and then if the edit distance suddenly increases significantly then I know there is a frameshift. But I'm having difficultly setting a normalized threshold for a significant increase in edit distance that works on ...
written 14 hours ago by Mensur Dlakic3.3k
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Comment: C: Customise blastn to exclude key words
... I don't think one can get blast to ignore keywords - it is a sequence search tool rather than keyword parser. Separately, I don't think it is a good idea to do what you want even if it was possible, as I know from experience that even genuine hits sometimes have words like `genome` or `predicted` in ...
written 1 day ago by Mensur Dlakic3.3k
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Answer: A: How to rename multiple fastq files
... Below is a shell script that replaces defined strings inside a group of files with the same extension. It is probably an overkill in your case since you can simply enter 4 `mv` commands instead of 2 needed with this script. First save the script as `fix-name.com` and make it executable (`chmod +x fi ...
written 1 day ago by Mensur Dlakic3.3k
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Answer: A: Problem with hmmpress for Superfamily_1.75 hmmlib
... It is almost certainly a mismatch between program versions, as SUPERFAMILY version 1.75 goes way back. Typing `head hmmlib_1.75` will tell you what version of HMMer was used. If you have the original alignments available, the models can be created from scratch using your current `hmmbuild` version. ...
written 1 day ago by Mensur Dlakic3.3k
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Answer: A: failed to installation
... This is a kind of error that is difficult to troubleshoot from the information you provided. Generally speaking, your compiler is probably too old (despite them saying than anything higher than `GCC 4.9` should work), or you are lacking proper program dependencies. You can save yourself lots of trou ...
written 2 days ago by Mensur Dlakic3.3k
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Answer: A: is there a problem with my block for mrbayes in CIPRES?
... I would have to see the whole `.log` file to be certain, but there is a good chance that nothing is wrong with your commands. This type of error will appear in at least two cases I know about: 1) when the run was continued after the interruption, and the resulting files don't have the same number of ...
written 3 days ago by Mensur Dlakic3.3k
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Answer: A: link between SCOPE and PFAM
... I am assuming that you are asking about SCOP or SCOPe. Generally speaking, Pfam and SCOP domain annotations are different. SCOP domain assignments are based on expert examination of folded units within structures, while Pfam domains are derived from sequence alignments. In many cases the two assign ...
written 5 days ago by Mensur Dlakic3.3k
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Comment: C: Struggling to work on a large Count Matrix
... Maybe I am missing your point. Do you see anything in the question that implies biology or bioinformatics application of what this poster is trying to do? My point was that lots of posters are turned away even though they sometimes have legitimate biology question that may be related to bioinformat ...
written 5 days ago by Mensur Dlakic3.3k
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Comment: C: blast with large deletion
... You may want to look at FASTA package - see this [**post**][1]. [1]: https://www.biostars.org/p/18533/#18662 ...
written 6 days ago by Mensur Dlakic3.3k

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