Forum: General
09-19-2012, 04:59 PM
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Replies: 1
Views: 2,024
KEGG vs MetaCyc
which one is a better tool for pathway annotation KEGG or MetaCyc?:(
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Forum: General
09-18-2012, 08:25 PM
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Replies: 5
Views: 1,426
prices?
Just a general question, what would be a fair price to pay to sequence (draft level) a bacterial genome (~10 Mb):). Trying to calculate a budget for a comparative study of several genomes.:confused:
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Forum: Bioinformatics
07-26-2012, 01:41 PM
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Replies: 0
Views: 1,863
fisher test, X test, Cramer’s V
I have three groups of fungal genes. These were obtained by presence and absence in non-pathogens, animal pathogens and plant-pathogens. I am trying to find any overepresented COG or pfam group in...
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Forum: Illumina/Solexa
06-29-2012, 09:00 AM
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Replies: 3
Views: 1,433
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Forum: Illumina/Solexa
06-29-2012, 08:03 AM
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Replies: 3
Views: 1,433
Real time of the whole process
I have been doing some research about prices and time for sequencing using any of the new technologies (ilumina/solexa, 454). Although in theory the sequencing reaction and all the additional...
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Forum: Bioinformatics
04-23-2012, 12:23 PM
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Replies: 3
Views: 1,556
Orthomcl does a good job. The software predicts...
Orthomcl does a good job. The software predicts orthology based on reciprocal blast. The output gives you a general picture of what you want. However for more specific details you want to reconstruct...
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Forum: Bioinformatics
03-19-2012, 11:53 AM
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Replies: 9
Views: 8,046
splitting big genbank file
I have a big gbk file containing multiple gbks, is there any simple way to split this big gbk into small gbks Thanks.
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Forum: General
08-17-2011, 12:11 PM
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Replies: 0
Views: 2,675
Phipack or other recombination detection program
I am trying to get the Phipack software implemented by Bruen et al. It seems that the link where the source is or was located is not working anymore. Does anybody has the sources of this program?....
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Forum: 454 Pyrosequencing
08-10-2011, 02:39 PM
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Replies: 9
Views: 4,363
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Forum: Bioinformatics
04-20-2011, 09:13 AM
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Replies: 0
Views: 1,790
Orthomcl warning message
I am running orthoMCL v1.4 and at the parsing step I am getting a warning message:
Argument "" isn't numeric in division (/) at /opt/local/lib/perl5/site_perl/5.8.9/Bio/Search/HSP/GenericHSP.pm...
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Forum: General
04-13-2011, 01:47 PM
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Replies: 0
Views: 1,436
Orthomcl warning message
I am running orthoMCL v1.4 and at the parsing step I am getting a warning message:
Argument "" isn't numeric in division (/) at /opt/local/lib/perl5/site_perl/5.8.9/Bio/Search/HSP/GenericHSP.pm...
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Forum: Bioinformatics
04-13-2011, 10:46 AM
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Replies: 0
Views: 1,575
Warning message in orthomcl v1.4
I am running orthoMCL v1.4 and at the parsing step I am getting a warning message:
Argument "" isn't numeric in division (/) at /opt/local/lib/perl5/site_perl/5.8.9/Bio/Search/HSP/GenericHSP.pm...
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Forum: Bioinformatics
04-04-2011, 10:48 AM
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Replies: 6
Views: 5,434
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Forum: Bioinformatics
03-22-2011, 03:35 PM
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Replies: 6
Views: 2,678
You could extract fasta and quality files from...
You could extract fasta and quality files from the sff files. Then you could use MIRA assembler. The information here.
http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page
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Forum: Bioinformatics
03-22-2011, 12:57 PM
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Replies: 5
Views: 8,275
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Forum: Bioinformatics
03-22-2011, 12:38 PM
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Replies: 3
Views: 3,293
Newbler
Hey Hinsby,
perhaps you could get some hints here:
http://biostar.stackexchange.com/questions/3749/newbler-and-ubuntu
If you are trying to assembly 454 maybe you could try MIRA. It works for me...
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Forum: Introductions
02-01-2010, 08:38 PM
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Replies: 3
Views: 1,405
Thanks for your comments,
Yeah I already did...
Thanks for your comments,
Yeah I already did some simulations with some programs (Velvet and ssake) in my old Mac Pro, 8 GB memory. It is fine with 2 million of reads (~50 bp length), but more than...
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Forum: Introductions
02-01-2010, 03:30 PM
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Replies: 3
Views: 1,405
Hello,
Hello There!
I am starting an evaluation of free softwares in order to assembly solexa reads. I have money to buy a new good computer. I've noticed that most of the software for assembling require...
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