Forum: Bioinformatics
05-14-2014, 12:11 AM
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Replies: 4
Views: 4,078
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Forum: Bioinformatics
12-24-2013, 12:25 AM
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Replies: 0
Views: 1,664
Differences between NONCODE and RFAM?
Dear colleagues, I'm annotating an eukaryotic genome and want to use INFERNAL (http://infernal.janelia.org/)+NONCODE (http://www.noncode.org/)/RFAM (http://rfam.sanger.ac.uk/) for annotation of...
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Forum: Bioinformatics
10-01-2013, 07:15 PM
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Replies: 3
Views: 2,141
They are more or less overlapping, though...
They are more or less overlapping, though sometimes only by a few AA. The amount of transmembrane domains is also the same in all estimates. This is actually all I need (how many domains there are...
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Forum: Bioinformatics
09-30-2013, 10:30 PM
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Replies: 3
Views: 2,141
Finding transmembrane domains
I need to locate transmembrane domains in a protein, so I've run it trough webservers linked at expasy in "Topology prediction" section (SOSUI, TMHMM, HMMTOP, etc.) And you know what? Every single...
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Forum: Bioinformatics
09-30-2013, 10:22 PM
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Replies: 3
Views: 4,206
Can anyone please explain me why the default...
Can anyone please explain me why the default behaviour is to randomly choose one of mappings? Making sense of multiple mappings is big enough headache without mapper hiding half the results from you.
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Forum: Bioinformatics
09-09-2013, 10:09 PM
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Replies: 3
Views: 3,115
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Forum: Bioinformatics
08-27-2013, 11:23 PM
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Replies: 5
Views: 2,104
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Forum: Bioinformatics
08-16-2013, 01:15 AM
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Replies: 2
Views: 2,751
I think I found what I was looking for, posting...
I think I found what I was looking for, posting here in case someone will find it useful. Brenda Enzymes DB (http://www.brenda-enzymes.org/soap2/) allows to get lots of enzyme information via SOAP...
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Forum: Bioinformatics
08-14-2013, 11:56 PM
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Replies: 2
Views: 2,751
Mapping reads against metabolical maps
I need to make a functional analysis of a metagenome and therefore have to map a lot of color space SOLiD reads 75 bp each (sadly, assembly isn't any good) against metabolical pathways. Desired...
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Forum: Bioinformatics
06-05-2013, 09:47 PM
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Replies: 10
Views: 3,801
If you want to do a taxonomic assignment for...
If you want to do a taxonomic assignment for ribosomal RNAs (metagenome or something), look at mothur package instead of BLAST. You will not have to parse results manually or write the script or...
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Forum: Bioinformatics
05-23-2013, 07:37 PM
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Replies: 2
Views: 1,379
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Forum: Bioinformatics
05-22-2013, 11:35 PM
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Replies: 2
Views: 1,379
Making Jalview less annoying?
Hello folks. My question is not science-related, but still: how to disable examlpe alignments, 3Ds and other assorted garbage popping up on launch of jalview?
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Forum: Bioinformatics
05-22-2013, 11:35 PM
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Replies: 4
Views: 2,204
If you only need several genes, you can gather...
If you only need several genes, you can gather them by hand. Download some sequence browser (I personally prefer artemis), look up hit location, strand and frame in blastx/tblasn output and copypaste...
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Forum: Bioinformatics
03-04-2013, 09:12 PM
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Replies: 7
Views: 4,308
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Forum: Bioinformatics
02-06-2013, 08:03 AM
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Replies: 12
Views: 7,411
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Forum: SOLiD
02-06-2013, 07:58 AM
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Replies: 4
Views: 8,779
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Forum: Bioinformatics
01-21-2013, 10:38 PM
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Replies: 2
Views: 3,338
Well, you use a bunch of methods and you get a...
Well, you use a bunch of methods and you get a bunch of different trees, that is usual. If you add, for instance, analysis of genomic rearrangements, you will get one more tree, some phenotypic...
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Forum: Metagenomics
01-21-2013, 10:08 PM
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Replies: 7
Views: 3,749
Thanks colindaven, neat papers, esp....
Thanks colindaven, neat papers, esp. genome-from-metagenome one. And yet I still have a question: is it even possible to use raw color-space reads (ie no assembly, no transforming to base space) to...
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Forum: Bioinformatics
10-07-2012, 07:11 PM
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Replies: 3
Views: 1,640
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Forum: Bioinformatics
09-27-2012, 12:19 AM
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Replies: 4
Views: 1,791
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Forum: Bioinformatics
09-19-2012, 07:41 PM
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Replies: 4
Views: 1,664
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Forum: Bioinformatics
09-19-2012, 07:33 PM
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Replies: 23
Views: 18,888
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Forum: Bioinformatics
09-19-2012, 07:22 PM
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Replies: 6
Views: 5,465
Kind of related question. Is there any tool to...
Kind of related question. Is there any tool to nicely visualize rearrangement scenario (e.g. reconstructed by MGR(A), COGNAC, GRAPPA, etc)? That is, I have ancestral genomes, sequence of operations...
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Forum: Bioinformatics
08-06-2012, 09:02 PM
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Replies: 4
Views: 1,634
BtW, why do you need a viewer for basic...
BtW, why do you need a viewer for basic alignments? If they are for further analysis (ie phylogenies, building some sort of models, etc) command-line tools like clustalw or muscle should be ok.
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Forum: Bioinformatics
08-02-2012, 12:30 AM
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Replies: 0
Views: 1,044
What is minimum spanning network?
I don't get it; Huson's book on networks says that it is a subgraph of network with pile of edges removed and then SplitsTree4 says it can build it from binary data. If it is what I think about, then...
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