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Forum: Bioinformatics 03-12-2013, 06:44 AM
Replies: 1
Views: 1,375
Posted By joshuapk
I lied, I wasn't counting the leaves as nodes. ...

I lied, I wasn't counting the leaves as nodes.
Thanks
Forum: Bioinformatics 03-12-2013, 06:35 AM
Replies: 1
Views: 1,375
Posted By joshuapk
Bioperl Tree Object

If anyone uses Bioperl Tree module out there I could use your help. I am finding that when I read in a .dnd file (newick) from a clustal alignment. Then count the number of nodes that exist within...
Forum: Bioinformatics 11-09-2012, 12:49 PM
Replies: 1
Views: 2,362
Posted By joshuapk
I would suggest either downloading the...

I would suggest either downloading the mitochondria Genbank files and parsing with Bio::Perl Feature-Annotation (http://www.bioperl.org/wiki/HOWTO:Feature-Annotation). Or if these genes have...
Forum: Bioinformatics 11-09-2012, 12:29 PM
Replies: 0
Views: 1,099
Posted By joshuapk
Metavelvet Histogram

Hello all I was wondering if anyone could explain to me what the Metavelvet coverage histogram means. http://metavelvet.dna.bio.keio.ac.jp/img/covHisto2.png

Also if anyone knows a way to retrieve...
Forum: Bioinformatics 06-07-2012, 11:03 AM
Replies: 1
Views: 1,824
Posted By joshuapk
Protein Secondary Structure Guided Alignments

So I need to make an alignment using secondary structure for gap penalties. I have found that Clustal is suppose to be able to do this but I try to follow their instructions...
Forum: Bioinformatics 06-04-2012, 05:59 AM
Replies: 6
Views: 5,473
Posted By joshuapk
Compatibility

I'll have to fight with it a bit to get it running since I am running Windows 7 64bit and 64bit JRE however thank you for the suggestion.
Forum: Bioinformatics 06-04-2012, 05:51 AM
Replies: 17
Views: 9,998
Posted By joshuapk
You may way to consider a CD-HIT run to lower...

You may way to consider a CD-HIT run to lower complexity again by removing duplicate reads. I suggest getting access to a cluster and using Celera Assembler however, remember that alot of your...
Forum: Bioinformatics 05-30-2012, 06:35 AM
Replies: 6
Views: 5,473
Posted By joshuapk
Recombination Detection Algorithms/Programs

Hello Everyone,
If we can let us start a thread that has all the recombination detection programs and algorithms with links and pros and cons. I'll start us off with the small list I have been...
Forum: Introductions 03-27-2012, 05:32 AM
Replies: 0
Views: 799
Posted By joshuapk
Hello from Joshua P Katz

I am a computationqal biologist working at University of Pittsburgh in Dr. Pipas' lab. We work mainly with SV40 and other Polyomaviridae, however, my job is to scour through every known viral genome...
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