User: cmdcolin

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cmdcolin680
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680
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Bioinformatics at MSU

Posts by cmdcolin

<prev • 141 results • page 1 of 15 • next >
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Comment: C: Rescaffolding a genome assembly?
... I wasn't able to do a really comprehensive comparison of all options but the "rescaffolding" option via running SSPACE using mate pair reads on the broken up contigs produced some new scaffolds that suggested a different arrangement of contigs (it stiched together contigs that were on different scaf ...
written 8 days ago by cmdcolin680
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Comment: C: Repeatmasker, Can't locate Text/Soundex.pm
... Have you tried installing repeatmasker using a simple package manager such as homebrew? `brew install homebrew/science/repeatmasker` works quite well on OSX for me ...
written 5 weeks ago by cmdcolin680
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Comment: C: Blast Xml For Multiple Databases
... It is definitely possible to do this without aliastool, as mentioned above, passing multiple arguments for db. It has the annoying consequence of not telling you "which" database a particular sequence came from though ...
written 6 weeks ago by cmdcolin680
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Comment: C: Ideal settings for blasting a protein/cdna against a genome?
... It would be same species or fairly closely related (e.g. getting a danio gene, blasting against fish of interest). I don't necessarily have exact use cases but there were biologists wanting to find the location of their gene of interest in a poorly annotated genome, and they had cdna sequences from ...
written 7 weeks ago by cmdcolin680
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Ideal settings for blasting a protein/cdna against a genome?
... Are there any ideal settings for BLAST to align a protein or cdna against a genome? Or is it perhaps even misleading to rely on BLAST this way and it's better to use something like exonerate (protein2genome/est2genome)? ...
exonerate blast written 7 weeks ago by cmdcolin680
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Comment: C: Rename an existing BLAST database
... My particular case the -title argument was also added to the makeblastdb command, and I was hoping to just simply modify the title that was given to the DB rather than regenerate everything with makeblastdb. In this case renaming the files wouldn't work I think since the -title was used. ...
written 7 weeks ago by cmdcolin680
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Rename an existing BLAST database
... Is it possible to rename an existing BLAST database using the NCBI command line tools? ...
blast written 7 weeks ago by cmdcolin680 • updated 7 weeks ago by st.ph.n1.6k
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Answer: A: List of np-hard problems in biology/bioinformatics
... Scaffolding as well as de novo assembly are formally NP hard but have many heuristics "The prevalence of heuristic choices in assembly owes its origins partly to several well-known early results regarding its computational complexity [1, 2] (and further confirmed by recent studies [3, 4]) which sug ...
written 9 weeks ago by cmdcolin680
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Comment: C: What is the difference between GTF AND GFF format
... The second link had weird formatting, here is the correct one for "2.2" http://mblab.wustl.edu/GTF22.html ...
written 10 weeks ago by cmdcolin680
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Comment: C: PERL: How I can "save information in a hash (%)"?
... Not to beat a dead horse, but if it is an assignment, it does not appear to say "use bioperl". You may find it better to use the perl by itself first before resorting to bioperl ...
written 11 weeks ago by cmdcolin680

Latest awards to cmdcolin

Appreciated 6 days ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Scholar 4 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 4 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Centurion 4 months ago, created 100 posts.
Appreciated 5 months ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Voter 9 months ago, voted more than 100 times.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 2.8 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 2.8 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
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