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Search: Posts Made By: Hel
Forum: Bioinformatics 03-09-2016, 07:16 AM
Replies: 3
Views: 1,012
Posted By Hel
Thanks GenoMax, but I do not want to download...

Thanks GenoMax, but I do not want to download everything, I rather need a site that allows the downloading of all the species names of a particular taxon/taxa (in my case: Bacteria, Archaea and...
Forum: Bioinformatics 03-09-2016, 06:23 AM
Replies: 3
Views: 1,012
Posted By Hel
Downloading all species names of Bacteria, Archaea and viruses

Hi there,

I would like to download all the species names of Bacteria, Archaea and Viruses. I can't find how to do this from NCBI website. Do you know any reliable website to do it?

Thanks in...
Forum: Bioinformatics 05-29-2015, 04:08 AM
Replies: 2
Views: 1,816
Posted By Hel
Count hits in Local Blast (Blast+)

Hi there,

I have just run a standard Local Blast using Blast+:
blastx -db mydb -query mysample -evalue 0.00001 -out blastxresult

and I wonder: How to check the number of blast hits?...
Forum: Bioinformatics 05-18-2015, 02:25 AM
Replies: 7
Views: 4,761
Posted By Hel
Thanks to all, I am very grateful for your help, ...

Thanks to all, I am very grateful for your help,

This is my opinion:

(i) CD-HIT seems interesting, but I have not test it yet.

(ii) Using 'cat', 'sort' and 'uniq' commands in FASTA files...
Forum: Bioinformatics 03-13-2015, 10:09 AM
Replies: 7
Views: 4,761
Posted By Hel
Compare fasta files

Hi there,

I want to compare several fasta files containing sequences. These sequences are transcripts obtained from RNA-Seq. I want to find out the shared transcripts between samples.
I cannot...
Forum: Bioinformatics 04-08-2014, 09:09 AM
Replies: 2
Views: 1,384
Posted By Hel
It works perfectly! Thank you very much GenoMax!

It works perfectly! Thank you very much GenoMax!
Forum: Bioinformatics 04-08-2014, 08:16 AM
Replies: 2
Views: 1,384
Posted By Hel
How to obtain gene ids from an .xml file

Hi all,

I have an .xml file from a blast search and I would like to extract the gene identifiers. Is it possible?

Thanks in advance,
Forum: Bioinformatics 04-02-2014, 03:21 AM
Replies: 3
Views: 1,422
Posted By Hel
You can try Blast2GO, it assigns GO terms to your...

You can try Blast2GO, it assigns GO terms to your sequences by first performing a blast.
Forum: Bioinformatics 03-27-2014, 06:47 AM
Replies: 1
Views: 801
Posted By Hel
Constructing a customized GO dataset

Hi all,

I would like to construct a customized dataset of a particular GO subset. For example, a list including the term "spermatogenesis" and all its child terms. Is it possible?
According to...
Forum: Bioinformatics 01-22-2014, 03:44 AM
Replies: 0
Views: 1,257
Posted By Hel
program similar to REVIGO, but that allows to explore the data afterwards?

Hi all,

Does anybody know a program similar to REVIGO, but that allows to explore the data afterwards? I would like to go into the GO groups and see the list of genes included en each of them.
...
Forum: Bioinformatics 01-17-2014, 06:08 AM
Replies: 9
Views: 1,854
Posted By Hel
Ok, thanks!

Ok, thanks!
Forum: Bioinformatics 01-17-2014, 03:53 AM
Replies: 9
Views: 1,854
Posted By Hel
Hey! How did you get your list of GO terms and...

Hey! How did you get your list of GO terms and p-values? I run blast2go, but I only got a list of GO terms, lacking the e-values… Thanks in advance!
Forum: Bioinformatics 01-10-2014, 05:24 AM
Replies: 1
Views: 1,226
Posted By Hel
Raw reads (from NGS) to perform a functional annotation analysis?

Hi all,

I have a theoretical question regarding functional annotation:

Is it correct to use raw reads (from NGS) to perform a functional annotation analysis?

Someone suggested me to use...
Forum: Bioinformatics 12-11-2013, 07:28 AM
Replies: 8
Views: 4,327
Posted By Hel
Thanks to all :). I'm sorry but I donīt...

Thanks to all :). I'm sorry but I donīt understand everything.

rhinoceros) Which tool to predict proteins?

sphill) Well, Blast2GO already do the blast step, isn't it?

mcnelson.phd) My...
Forum: Bioinformatics 12-10-2013, 03:50 AM
Replies: 8
Views: 4,327
Posted By Hel
Hi NGS_New_User, I also have the same...

Hi NGS_New_User,

I also have the same question. I have a de novo assembled transcriptome to analyze in gene ontology terms. Please maubp, could you explain how to get genes/proteins from our...
Forum: Bioinformatics 12-04-2013, 08:32 AM
Replies: 1
Views: 1,142
Posted By Hel
How to download a database restricted to genes of insects (Hexapoda)?

Hi all,

I would like to download a NCBI database, but restricted to insects (Hexapoda). Is it possible?

I will appreciate your feedback.

Thanks in advance,
Forum: Bioinformatics 11-22-2013, 02:40 AM
Replies: 6
Views: 2,330
Posted By Hel
I tried it with another file of similar size. In...

I tried it with another file of similar size. In this case it results in 21 files in several formats (.annot, .dat, .png, .jpg and .svg) instead.
I don't understand why in the first case I only...
Forum: Bioinformatics 11-21-2013, 03:55 AM
Replies: 6
Views: 2,330
Posted By Hel
Ok, thanks. So the problem may be the large...

Ok, thanks. So the problem may be the large dataset..
Forum: Bioinformatics 11-20-2013, 02:38 AM
Replies: 6
Views: 2,330
Posted By Hel
b2g4pipe v2.5.0

b2g4pipe v2.5.0
Forum: Bioinformatics 11-06-2013, 08:21 AM
Replies: 6
Views: 2,330
Posted By Hel
b2g4pipe returns only a .annot file... What about the .dat file?

Hi all,

After running b2g4pipe, I only got a .annot file in the "results" directory. Is that all? What about the .dat file? I cannot find it.

The command I utilized was:
java -Xmx4000m -cp...
Forum: Bioinformatics 07-31-2013, 09:23 AM
Replies: 7
Views: 2,200
Posted By Hel
Thanks to all, So it's better to use Blast+...

Thanks to all,
So it's better to use Blast+ than Blastall, right? Then I will try to find the Blast+ tutorial. About what to do with 50,000 query sequences...well, of course I've though about it. I...
Forum: Bioinformatics 07-31-2013, 03:57 AM
Replies: 4
Views: 8,134
Posted By Hel
Thanks! I will explore these options ;)

Thanks! I will explore these options ;)
Forum: Bioinformatics 07-31-2013, 03:56 AM
Replies: 7
Views: 2,200
Posted By Hel
How to perform a BLAST of many sequences?

Hi all,

I have about 50,000 sequences that need a BLAST, is it possible to perform a BLAST search of they all in one step?

Thanks
Forum: Bioinformatics 07-10-2013, 07:40 AM
Replies: 4
Views: 8,134
Posted By Hel
Is there any free tool similar to Blast2go?

Hi all,
Is there any free tool similar to Blast2go?
I've just started my PhD on NGS, in a non model species of insects (belonging to Coleopterans). I've just received a large amount of sequences...
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