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Forum: Pacific Biosciences 07-02-2019, 03:56 AM
Replies: 1
Views: 779
Posted By Antony03
Import a BAM file into SMRT Link

Hello everyone,

I just sequenced bacterial genomes by PacBio Sequel. Compared to the RS II technology, I received a BAM file from the sequencing platform. I would like to import my sequencing data...
Forum: Pacific Biosciences 04-10-2018, 10:49 AM
Replies: 1
Views: 2,333
Posted By Antony03
Assembly of a mycete genome with HGAP4

Hello,

I need to assemble a fungus genome for which no information is known. When doing the assembly with canu, I get an assembly of 4918 contigs with a total of 57 123 496 bp. However, with...
Forum: Bioinformatics 08-17-2015, 07:04 AM
Replies: 1
Views: 451
Posted By Antony03
A little up!

A little up!
Forum: Bioinformatics 08-11-2015, 06:24 AM
Replies: 1
Views: 451
Posted By Antony03
Own substitution matrix

Hi,

I would like to generate my own substitution matrices (nucleotides and amino acids) using multiple alignments. I'd like your opinion on how to generate these matrices.

Thank you :)
Forum: Bioinformatics 05-18-2015, 08:57 AM
Replies: 1
Views: 827
Posted By Antony03
tblastn bug?

Hello,

I have a problem with tblastn. I tried to research this protein sequence:

>BN1129_RS00085
MNKVLVAGILGLMLTACGQKEEAAAPAATPAADVAATVEQAASEATSTVEKVASEATATVEKAVSKAEAAVSDAKAN

In the draft...
Forum: Bioinformatics 05-11-2015, 05:03 PM
Replies: 2
Views: 2,058
Posted By Antony03
BWA - read identity

Hi,

I'm using BWA to map my short sequencing reads (Illumina MiSeq) on a reference sequence. Is this possible to set the minimum % of identity with BWA? For exemple, if I set 90%, then all reads...
Forum: General 04-01-2015, 03:07 PM
Replies: 1
Views: 1,917
Posted By Antony03
too high sequencing coverage

Hi,

I sequenced by Illumina MiSeq some phage genomes. Normally, with bacterial genomes, I have an average sequencing coverage of 75-90x. But with the phages (much more small genomes) the coverages...
Forum: Bioinformatics 02-08-2015, 03:31 AM
Replies: 1
Views: 841
Posted By Antony03
Is a bioinformatics tool to list mutations between two short bacterial sequences?

Hello,

I have two bacterial sequences of 10 kbp in fasta format and I am looking for a bioinformatics tool which is able to list the mutations (Indels and point mutations) between both sequences....
Forum: Bioinformatics 12-16-2014, 03:38 AM
Replies: 4
Views: 1,366
Posted By Antony03
Hello GenoMax, Thank you for your answer....

Hello GenoMax,

Thank you for your answer. The thread does not really seems helpful for me. I have >1000 sequences in amino acids, is there a way to perform a "blast-like" alignment to get the COG...
Forum: Bioinformatics 12-15-2014, 02:41 PM
Replies: 4
Views: 1,366
Posted By Antony03
Please, a little up!

Please, a little up!
Forum: Bioinformatics 12-11-2014, 03:32 PM
Replies: 4
Views: 1,366
Posted By Antony03
COG categories of protein sequences

Hello,

I have protein sequences and I would like to know the COG category for each sequence. What is the best procedure?

Sincerely,

Antony
Forum: General 10-04-2014, 06:39 AM
Replies: 1
Views: 668
Posted By Antony03
Are you sure that the papers refer to complete...

Are you sure that the papers refer to complete genomes and not only to some coding genes?
Forum: Bioinformatics 10-04-2014, 06:31 AM
Replies: 4
Views: 1,418
Posted By Antony03
Just a little up. I have the same question.

Just a little up. I have the same question.
Forum: General 10-04-2014, 06:29 AM
Replies: 3
Views: 2,087
Posted By Antony03
You should take a look at UGENE. I know this tool...

You should take a look at UGENE. I know this tool can produces consensus with a graphical interface and in command line.

http://ugene.unipro.ru
Forum: General 10-03-2014, 05:47 PM
Replies: 1
Views: 888
Posted By Antony03
How to correct a ref seq using Illumina

Dears colleagues,

Last year, I made the assembly of a complete bacterial genome using 454 sequencing reads. However, as you probably know, 454 technology is prone to frameshift. Consequently, I...
Forum: Bioinformatics 08-07-2014, 03:03 PM
Replies: 1
Views: 1,418
Posted By Antony03
fasta35 VS fasta36

Hello,

I need to use, for a specific job, fasta35 and not fasta36. However, the result is clearly not the same between both.

fasta35 gives only 1 alignment: http://pastebin.com/f4NdYJCt
...
Forum: Bioinformatics 07-27-2014, 09:05 AM
Replies: 6
Views: 1,011
Posted By Antony03
Thank you the answer. But, how can I make a local...

Thank you the answer. But, how can I make a local alignment with the resulting consensus? Is fasta36 or blast can handle it?
Forum: Bioinformatics 07-26-2014, 04:07 AM
Replies: 6
Views: 1,011
Posted By Antony03
Ideally, I would like to try both.

Ideally, I would like to try both.
Forum: Bioinformatics 07-25-2014, 03:26 PM
Replies: 6
Views: 1,011
Posted By Antony03
Pairwise alignment from a consensus in query

Hello,
I want to look for a specific gene in a genome sequence. The gene sequence is degenerate and a colleague has suggested that I should make a multiple alignment of orthologous genes, make a...
Forum: Bioinformatics 07-25-2014, 03:25 PM
Replies: 1
Views: 923
Posted By Antony03
When you load your tree, a box should appear and...

When you load your tree, a box should appear and ask you how you want to call the values (label by default). At your left, there are some options (node, branch ...) you make your choice there.
Forum: General 07-20-2014, 01:51 PM
Replies: 2
Views: 2,716
Posted By Antony03
% of similarity to be orthologous

Hello,

I have a philosophic question: What is the minimum similarity (% of amino acids) to consider two genes orthologous? Are there some studies about that?

Thank you :)
Forum: Bioinformatics 03-05-2014, 05:26 PM
Replies: 3
Views: 1,092
Posted By Antony03
Annotation of a bacterial genome

Hi,

I'm pretty sure that this question was already ask many times but I don't find any post with clear answers. I'm looking for an annotation tool for a bacterial chromosome and plasmids. What is...
Forum: Bioinformatics 02-12-2014, 03:32 AM
Replies: 2
Views: 1,291
Posted By Antony03
But, is it possible with Artemis to have a single...

But, is it possible with Artemis to have a single file that contains both (sequence and annotations)?
Forum: Bioinformatics 02-09-2014, 04:09 PM
Replies: 2
Views: 1,291
Posted By Antony03
Complete .gbk with Artemis

Hi,

I'm using Artemis for annotated a little genome fragment (50 kb). I can save my sequence in gbk and my ORFs in other gbk file, but is this possible to have a complete .gbk (sequence + ORFs)?
...
Forum: Bioinformatics 11-13-2013, 04:30 PM
Replies: 2
Views: 952
Posted By Antony03
A little up! Please :)

A little up!

Please :)
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