SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 40
Search took 0.02 seconds.
Search: Posts Made By: A_Morozov
Forum: Bioinformatics 05-13-2014, 11:11 PM
Replies: 4
Views: 3,645
Posted By A_Morozov
The same bug with Blast 2.2.26 on Linux Mint 15. ...

The same bug with Blast 2.2.26 on Linux Mint 15.
Just in case someone still encounters it, it seems to occur only with multiple processors (ie -a >=2), so you can avoid it at the price of longer...
Forum: Bioinformatics 12-23-2013, 11:25 PM
Replies: 0
Views: 1,410
Posted By A_Morozov
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...
Forum: Bioinformatics 10-01-2013, 06:15 PM
Replies: 3
Views: 1,874
Posted By A_Morozov
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...
Forum: Bioinformatics 09-30-2013, 09:30 PM
Replies: 3
Views: 1,874
Posted By A_Morozov
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...
Forum: Bioinformatics 09-30-2013, 09:22 PM
Replies: 3
Views: 3,971
Posted By A_Morozov
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.
Forum: Bioinformatics 09-09-2013, 09:09 PM
Replies: 3
Views: 2,857
Posted By A_Morozov
Yeah, one more thing to keep in mind. E-value...

Yeah, one more thing to keep in mind. E-value setting does not affect parameters of the alignment, it just makes BLAST display more or less hits.
Forum: Bioinformatics 08-27-2013, 10:23 PM
Replies: 5
Views: 1,788
Posted By A_Morozov
Perhaps you could just extract informative sites...

Perhaps you could just extract informative sites and use just them like SNPs, since computational burden of analyzing megabases via ML or bayesian inference is tremendous, and most sequence doesn't...
Forum: Bioinformatics 08-16-2013, 12:15 AM
Replies: 2
Views: 2,237
Posted By A_Morozov
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...
Forum: Bioinformatics 08-14-2013, 10:56 PM
Replies: 2
Views: 2,237
Posted By A_Morozov
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...
Forum: Bioinformatics 06-05-2013, 08:47 PM
Replies: 10
Views: 3,185
Posted By A_Morozov
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...
Forum: Bioinformatics 05-23-2013, 06:37 PM
Replies: 2
Views: 1,158
Posted By A_Morozov
No such button in the preferences tab. Already...

No such button in the preferences tab. Already tried fiddling with nearly any setting to no effect. Anyway, thanks for the mailing list link.
Forum: Bioinformatics 05-22-2013, 10:35 PM
Replies: 2
Views: 1,158
Posted By A_Morozov
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?
Forum: Bioinformatics 05-22-2013, 10:35 PM
Replies: 4
Views: 1,970
Posted By A_Morozov
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...
Forum: Bioinformatics 03-04-2013, 08:12 PM
Replies: 7
Views: 3,478
Posted By A_Morozov
No fun, guys. Baika might be (and claims to be in...

No fun, guys. Baika might be (and claims to be in introduction section) a non-bioniformatitian stuck with what is not his/her area of expertise. If you went to genomics/bioinformatics lab, you should...
Forum: Bioinformatics 02-06-2013, 07:03 AM
Replies: 12
Views: 6,758
Posted By A_Morozov
Same stuff as in urchgene's post observed with...

Same stuff as in urchgene's post observed with velvet 1.2.08.

Seems like a problem is just a lack of RAM. I moved to cluster with more of it and everything works fine. Would be nice if velvet...
Forum: SOLiD 02-06-2013, 06:58 AM
Replies: 4
Views: 6,577
Posted By A_Morozov
Conversion is clearly wrong. If my memory serves,...

Conversion is clearly wrong. If my memory serves, ! is zero quality in Sanger-type fastq, and dots are missing colors (which are either 0 or -1 quality depending on version of the machine). Are...
Forum: Bioinformatics 01-21-2013, 09:38 PM
Replies: 2
Views: 3,028
Posted By A_Morozov
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...
Forum: Metagenomics 01-21-2013, 09:08 PM
Replies: 7
Views: 3,324
Posted By A_Morozov
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...
Forum: Bioinformatics 10-07-2012, 06:11 PM
Replies: 3
Views: 1,348
Posted By A_Morozov
For start, you can just call pairs of genes with...

For start, you can just call pairs of genes with alignment score above certain treshold common, and call those that don't have such pairing unique. This is grossly oversimplified approach, because...
Forum: Bioinformatics 09-26-2012, 11:19 PM
Replies: 4
Views: 1,533
Posted By A_Morozov
May I ask a noobish question? Is it 5 reads as in...

May I ask a noobish question? Is it 5 reads as in "Five pieces of DNA sequence being read by some method" and if yes, how did you end up assembling it? No insult meant, I'm really curious.
Forum: Bioinformatics 09-19-2012, 06:41 PM
Replies: 4
Views: 1,456
Posted By A_Morozov
What exactly kind of comparison do you need? If...

What exactly kind of comparison do you need? If it's just synteny blocks (ie ones with conserved order across set of genomes), pick MAUVE. If you want to reconstruct some phylogeny using genomic...
Forum: Bioinformatics 09-19-2012, 06:33 PM
Replies: 23
Views: 17,277
Posted By A_Morozov
Are those specialised bioinformatics distros any...

Are those specialised bioinformatics distros any good? I mean, you can print something like "sudo apt-get install bioperl" (which by the way drags lots of basic tools like aligners, blast and some...
Forum: Bioinformatics 09-19-2012, 06:22 PM
Replies: 6
Views: 4,970
Posted By A_Morozov
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...
Forum: Bioinformatics 08-06-2012, 08:02 PM
Replies: 4
Views: 1,356
Posted By A_Morozov
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.
Forum: Bioinformatics 08-01-2012, 11:30 PM
Replies: 0
Views: 890
Posted By A_Morozov
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...
Showing results 1 to 25 of 40

 


All times are GMT -8. The time now is 06:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO