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Forum: Bioinformatics 02-14-2012, 06:20 AM
Replies: 2
Views: 1,475
Posted By andreitudor
Thank you. Do you know any articles that discuss...

Thank you. Do you know any articles that discuss this subject? Illumina substitutions?
Forum: Bioinformatics 02-13-2012, 07:09 AM
Replies: 2
Views: 1,475
Posted By andreitudor
Question Illumina insertions deletions

Hello,

Is it safe to assume that a higher coverage tends to resolve the nt-substitutions that can occur in Illumina sequencing?
Forum: Bioinformatics 10-27-2011, 08:36 PM
Replies: 2
Views: 3,925
Posted By andreitudor
Talking Bioinformatics libraries for C++

Hello,

I was wondering if it would interest the community a well maintained and accurate bioinformatics library for C++. I am thinking of starting a project like this, but I would like to know if...
Forum: Bioinformatics 04-15-2011, 04:25 PM
Replies: 6
Views: 3,319
Posted By andreitudor
Yes indeed, I have those files. I have the .sff...

Yes indeed, I have those files. I have the .sff file, so I have the multi-fasta of the reads, .qual for the reads, and an assembly with newbler. in the newbler assembly directory i have the fasta and...
Forum: Bioinformatics 04-15-2011, 06:39 AM
Replies: 6
Views: 3,319
Posted By andreitudor
NGS reads quality

Is there a way to find a quality score for a 454 sequence?
I know I have the fasta and qual files, but can I get like a number for every read or all the reads together?

Andrei

EDIT: By reads...
Forum: Bioinformatics 04-07-2011, 06:29 AM
Replies: 0
Views: 2,011
Posted By andreitudor
Unhappy Staden install on Mac OSX 10.6

Hello,
I am trying to install staden on mac osx 10.6. I have successfully installed everything with macports, and have configured with the appropriate options. But when I $sudo make I get this...
Forum: Bioinformatics 03-28-2011, 08:14 AM
Replies: 0
Views: 1,236
Posted By andreitudor
Blast+ question

If i use a multifasta file as a query for blastn is there a way to choose only to search for a specific sequence from that file?
Forum: Bioinformatics 03-16-2011, 07:01 AM
Replies: 1
Views: 1,359
Posted By andreitudor
Gene extraction software

Hi,

I am looking for a tool in perl/bioperl for extracting the gene information from a genbank file. Anyone has any ideas?
Forum: Bioinformatics 03-07-2011, 04:39 AM
Replies: 23
Views: 18,369
Posted By andreitudor
I use Bio-Linux 6. It is based on ubuntu, but is...

I use Bio-Linux 6. It is based on ubuntu, but is developped specifically for bioinformatics by NEBC. It has a lot of software already installed. Of course you have to update some of the tools, but...
Forum: Bioinformatics 03-03-2011, 07:26 AM
Replies: 4
Views: 2,915
Posted By andreitudor
And how do I do that? The computer that I am...

And how do I do that? The computer that I am working from has no internet connection, so I have to download all the genbank files that contain the gene information. I can make a local database from...
Forum: Bioinformatics 03-03-2011, 06:57 AM
Replies: 4
Views: 2,915
Posted By andreitudor
OK, so blast+ does not do this automatically....

OK, so blast+ does not do this automatically. Then I should be able to do this with bioperl. There should be an object that can get the genbank information from a file and then you could compare it...
Forum: Bioinformatics 03-02-2011, 06:05 AM
Replies: 4
Views: 8,839
Posted By andreitudor
These sorts of conversions are rather tricky...

These sorts of conversions are rather tricky because it is difficult to construct a set of standard conversion decisions that will please everyone's specific demands. VCF to BED/GFF is doable with...
Forum: Bioinformatics 03-02-2011, 05:46 AM
Replies: 4
Views: 2,915
Posted By andreitudor
Question Blast+ database with gene annotation

Hello,

I have been trying for the last few days to make a blast database (with blast+ tools) that would contain the gene information from a genebank file. Is it possible to do that with blast+ or...
Forum: Bioinformatics 02-24-2011, 08:28 AM
Replies: 5
Views: 1,360
Posted By andreitudor
Thanks for the link. I do not have illumina...

Thanks for the link. I do not have illumina reads. Only 454.
Forum: Bioinformatics 02-24-2011, 08:07 AM
Replies: 5
Views: 1,360
Posted By andreitudor
I have the contigs assembled from the 454 data....

I have the contigs assembled from the 454 data. Would that be ok?
Forum: Bioinformatics 02-24-2011, 08:05 AM
Replies: 0
Views: 951
Posted By andreitudor
Perl/Tk question

I am making a database manager in Perl/Tk. I would like that when I press a button (btn1) a text box and a label appear in a frame below the button. The actuall problem is that when I press a second...
Forum: Bioinformatics 02-24-2011, 07:51 AM
Replies: 5
Views: 1,360
Posted By andreitudor
I am interested in IMAGE2, as I have some...

I am interested in IMAGE2, as I have some sequences on which I need to close the gaps. The question I have is does it work on 454 data or only on Illumina?
Forum: Bioinformatics 02-18-2011, 08:04 AM
Replies: 27
Views: 12,702
Posted By andreitudor
Hey guys, I have installed amos cvs on my...

Hey guys,

I have installed amos cvs on my ubuntu 10.04 64. I followed the tutorial of F-flow. The only problem is that when I try to lunch hawkeye from the console it says that the program does...
Forum: Bioinformatics 02-17-2011, 07:01 AM
Replies: 27
Views: 46,422
Posted By andreitudor
Hey guys, Thanks for your answers. I do not...

Hey guys,

Thanks for your answers. I do not want to use the tools provided from blast+ because I want to do it on my own. I looked into BIO:: DB:Fasta and I decided to use it, since it has a...
Forum: Bioinformatics 02-16-2011, 08:28 AM
Replies: 27
Views: 46,422
Posted By andreitudor
Extract sequence from multi fasta file with PERL

Hello,

I want to make a script that will extract a sequence from a multifasta file. I have made a file with 19 genomes from NCBI and I want to be able to extract a genome that I need from it. I...
Forum: Introductions 02-16-2011, 08:06 AM
Replies: 0
Views: 779
Posted By andreitudor
Talking Hello everyone!

Hi,

I'm new to this forum, and to the field of bioinformatics. I am a bioinformatics student. I found this site while searching for some information on the internet, and I find it very usefull....
Showing results 1 to 21 of 21

 


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