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Search: Posts Made By: Daniel Fernandez
Forum: Bioinformatics 05-13-2016, 09:33 AM
Replies: 15
Views: 6,994
Posted By Daniel Fernandez
Sorry I don't work on windows, but I search and I...

Sorry I don't work on windows, but I search and I think is findstr, I never test this. look these links.

http://www.mkyong.com/linux/grep-for-windows-findstr-example/...
Forum: Bioinformatics 05-06-2016, 07:20 AM
Replies: 15
Views: 6,994
Posted By Daniel Fernandez
p3_out.pl never worked, I did manually with...

p3_out.pl never worked, I did manually with egrep, with this I can solve.
Forum: Bioinformatics 02-21-2016, 07:39 AM
Replies: 15
Views: 6,994
Posted By Daniel Fernandez
I try to install it in my laptop but in the...

I try to install it in my laptop but in the process it show me error, I used biolinux in my lab, it have installed by default.
Well with the *.p3out I extract the primers and other parameters with...
Forum: Bioinformatics 02-19-2016, 07:48 AM
Replies: 15
Views: 6,994
Posted By Daniel Fernandez
I did that, but it show me the same Use of...

I did that, but it show me the same

Use of uninitialized value $count in concatenation (.) or string at ./p3_out.pl line 76, <SRC> chunk 11.

Primer modelling was successful for sequences....
Forum: Bioinformatics 02-18-2016, 07:29 PM
Replies: 15
Views: 6,994
Posted By Daniel Fernandez
yes! now when I run primer3_core the *.p3out show...

yes! now when I run primer3_core the *.p3out show me the primers:

But when I run p3_out.pl the *.result file doesn't show me the complete table with the primers:

./p3_out.pl FASTA.fa.p3out...
Forum: Bioinformatics 02-18-2016, 06:31 AM
Replies: 15
Views: 6,994
Posted By Daniel Fernandez
The *.misa file is Ok: ID SSR nr. SSR...

The *.misa file is Ok:

ID SSR nr. SSR type SSR size start end
Seq 1 p2 (TA)7 14 8423 8436
Seq 2 p2 (AC)8 16 21149 21164
Seq 3 c (AT)13(GT)10 46 21525 21570...
Forum: Bioinformatics 02-17-2016, 02:24 PM
Replies: 15
Views: 6,994
Posted By Daniel Fernandez
Yes you're right, the problem is in ./p3_out.pl...

Yes you're right, the problem is in ./p3_out.pl FASTA.fa.p3out FASTA.fa.misa

It show me this:

Use for uninitialized value $count in concatenation (.) or string at ./p3_out.pl line 76, <SRC>...
Forum: Bioinformatics 02-16-2016, 04:50 PM
Replies: 15
Views: 6,994
Posted By Daniel Fernandez
Primer3 primer3_core failed (SOLVED)

Hi, I select 11 microsatellites generated by MISA program (http://pgrc.ipk-gatersleben.de/misa/), now I want to design primer, and I use this.

misa.pl FASTA.fa
p3_in.pl FASTA.fa.misa...
Forum: Bioinformatics 04-25-2014, 09:48 AM
Replies: 9
Views: 3,433
Posted By Daniel Fernandez
Bioperl error in bacterial annotation

Hi, I installed PROKKA (http://www.vicbioinformatics.com/software.prokka.shtml) pipeline for annotation of a bacterial genome. One of its dependencies is BioPerl, I installed this according to...
Forum: Bioinformatics 09-23-2013, 02:47 PM
Replies: 0
Views: 1,573
Posted By Daniel Fernandez
Glimmer: Multifasta analysis

Hi everyone.
I am new user at glimmer. We have a bacterial genome in multifasta, contigs. We can predict the ORF, if we could a complete genome in one fasta, we could, but we with Multifasta, we can...
Forum: Bioinformatics 08-16-2013, 11:45 AM
Replies: 0
Views: 1,566
Posted By Daniel Fernandez
Genome in SRA

Hi,
I have to find some members of gene's family, in a genome in SRA format, (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP014648).
Well I convert this SRA to FastQ (fastq-dump) and then...
Forum: Bioinformatics 06-28-2013, 09:20 AM
Replies: 3
Views: 2,107
Posted By Daniel Fernandez
Well, this is the link...

Well, this is the link (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP014648), it is 454 (http://www.ncbi.nlm.nih.gov/sra/SRX172665).
This genome is in SRA and I converted to fastq and...
Forum: Bioinformatics 06-27-2013, 04:21 PM
Replies: 3
Views: 2,107
Posted By Daniel Fernandez
Assembly with Reference Sequence

Hi, anybody can tell me about one program to assembly with a reference sequence (in Linux)
I use CAP3 but this can't use a reference sequence.

Well I need assembly more than 300 million, so I...
Forum: Bioinformatics 09-13-2012, 01:50 PM
Replies: 23
Views: 18,473
Posted By Daniel Fernandez
1) Is Scientific Linux any good for...

1) Is Scientific Linux any good for bioinformatics? If yes, why?
No, a good bioinformatician is who know how to analyze the sequences and interpreted the results, not who know Linux, Linux is only a...
Forum: Bioinformatics 06-11-2012, 04:51 PM
Replies: 2
Views: 2,420
Posted By Daniel Fernandez
Well thanks but I did not find the converter...

Well thanks but I did not find the converter there, where is it?
Forum: Bioinformatics 06-09-2012, 11:41 PM
Replies: 2
Views: 2,420
Posted By Daniel Fernandez
Annotation in GFF3

Hi,

Can anybody tell me a program to find genes by homology that generate GFF3?

I tired AAT but only show me a table
I tried Exonerate but it give me a GFF2 and it can't load in artemis
If...
Forum: Bioinformatics 06-07-2012, 01:16 PM
Replies: 1
Views: 3,723
Posted By Daniel Fernandez
Annotation: Glimmer to GFF

Hi,

We tried to work with Glimmer for prokaryotes annotation, but we need a GFF format to load in Artemis.
anybody can tell me
How can I convert the glimmer out to GFF3 format, please?
...
Forum: Bioinformatics 06-05-2012, 07:33 PM
Replies: 0
Views: 2,428
Posted By Daniel Fernandez
Exonerate GFF in Artemis

Hi,

May be this is very simple question, I'm beginner in bioinformatics.

I'm trying to run exonerate, I tested with a partial chr1 of A. thaliana, and extract its mRNA, only for test. I...
Forum: Bioinformatics 02-15-2012, 09:16 AM
Replies: 1
Views: 1,970
Posted By Daniel Fernandez
Solved

SOLVED ok I write to the author and my error was only write ./configure , I did the exactly building with the --prefix=pwd and when I finished all installation, I copy all executables to...
Forum: Bioinformatics 02-10-2012, 03:00 PM
Replies: 1
Views: 1,970
Posted By Daniel Fernandez
AAT (analysis and annotation of genomes) - error

Hi everyone.

I'm trying to analysing a mammalian genome by the AAT package (http://aatpackage.sourceforge.net/), the package comes with examples (only I have to run the script runMe.sh) but don't...
Forum: Bioinformatics 11-29-2011, 09:25 PM
Replies: 0
Views: 1,792
Posted By Daniel Fernandez
TGICL fasta vs refdb

Hi,

I'm using tgicl for clustering EST,
I don't want to it perform all-vs-all, I want to it perform my EST against TIGR gene index <refDb>, how I can do that?.

I use

tgicl -F myEST.fasta...
Forum: Bioinformatics 11-26-2011, 10:45 PM
Replies: 30
Views: 14,299
Posted By Daniel Fernandez
Well, when I run the tgicl, the first cluster...

Well, when I run the tgicl, the first cluster have more than 1700 reads (and these are assembled in more than 200 contigs) and the rest have less than 100 reads.

I only run: tgicl AlpEST.fasta
...
Forum: Bioinformatics 11-24-2011, 07:19 AM
Replies: 30
Views: 14,299
Posted By Daniel Fernandez
I do that you tell me, but when I wrote...

I do that you tell me, but when I wrote ./configure the last line have a error

$ ./configure
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu...
Forum: Bioinformatics 11-23-2011, 09:12 AM
Replies: 30
Views: 14,299
Posted By Daniel Fernandez
TGICL installation (SOLVED)

Thanks very much, sorry for a lot of question, finally it run ...

But only one question more, it's about packages, you tell me about libfile-homedir-perl, I try other method (sudo dpkg -i...
Forum: Bioinformatics 11-22-2011, 07:58 AM
Replies: 30
Views: 14,299
Posted By Daniel Fernandez
Thanks, it works but 1. Is it necessary to...

Thanks, it works but

1. Is it necessary to write the input in the tgicl.cfg?
DB_FILE = AlpEST.fasta
Because I thought it work only with "tgicl AlpEST.fasta" (apart from other parameters)

2....
Showing results 1 to 25 of 31

 


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