SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 18 of 18
Search took 0.00 seconds.
Search: Posts Made By: joscarhuguet
Forum: General 09-19-2012, 04:59 PM
Replies: 1
Views: 2,024
Posted By joscarhuguet
KEGG vs MetaCyc

which one is a better tool for pathway annotation KEGG or MetaCyc?:(
Forum: General 09-18-2012, 08:25 PM
Replies: 5
Views: 1,426
Posted By joscarhuguet
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:
Forum: Bioinformatics 07-26-2012, 01:41 PM
Replies: 0
Views: 1,863
Posted By joscarhuguet
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...
Forum: Illumina/Solexa 06-29-2012, 09:00 AM
Replies: 3
Views: 1,433
Posted By joscarhuguet
agree ...so genome sequencing is not a "trivial...

agree ...so genome sequencing is not a "trivial lab-thing" yet, and scientific journals should give more credit for genome publications.
Forum: Illumina/Solexa 06-29-2012, 08:03 AM
Replies: 3
Views: 1,433
Posted By joscarhuguet
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...
Forum: Bioinformatics 04-23-2012, 12:23 PM
Replies: 3
Views: 1,556
Posted By joscarhuguet
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...
Forum: Bioinformatics 03-19-2012, 11:53 AM
Replies: 9
Views: 8,046
Posted By joscarhuguet
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.
Forum: General 08-17-2011, 12:11 PM
Replies: 0
Views: 2,675
Posted By joscarhuguet
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?....
Forum: 454 Pyrosequencing 08-10-2011, 02:39 PM
Replies: 9
Views: 4,363
Posted By joscarhuguet
MIRA is a nice assembler but that I understand is...

MIRA is a nice assembler but that I understand is that you used 454 first and now you want to improve your assembly with ilumina. That you will obtain is a better resolution for point mutations...
Forum: Bioinformatics 04-20-2011, 09:13 AM
Replies: 0
Views: 1,790
Posted By joscarhuguet
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...
Forum: General 04-13-2011, 01:47 PM
Replies: 0
Views: 1,436
Posted By joscarhuguet
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...
Forum: Bioinformatics 04-13-2011, 10:46 AM
Replies: 0
Views: 1,575
Posted By joscarhuguet
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...
Forum: Bioinformatics 04-04-2011, 10:48 AM
Replies: 6
Views: 5,434
Posted By joscarhuguet
You could try Artemis. ...

You could try Artemis.

http://www.sanger.ac.uk/resources/software/artemis/
Forum: Bioinformatics 03-22-2011, 03:35 PM
Replies: 6
Views: 2,678
Posted By joscarhuguet
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
Forum: Bioinformatics 03-22-2011, 12:57 PM
Replies: 5
Views: 8,275
Posted By joscarhuguet
There are some tools for manipulating gff files; ...

There are some tools for manipulating gff files;
If you have a little of experience with perl you could use them.

http://biowiki.org/GffTools#GFF_tools
Forum: Bioinformatics 03-22-2011, 12:38 PM
Replies: 3
Views: 3,293
Posted By joscarhuguet
Talking 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...
Forum: Introductions 02-01-2010, 08:38 PM
Replies: 3
Views: 1,405
Posted By joscarhuguet
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...
Forum: Introductions 02-01-2010, 03:30 PM
Replies: 3
Views: 1,405
Posted By joscarhuguet
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...
Showing results 1 to 18 of 18

 


All times are GMT -8. The time now is 05:56 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO