Arthur Fernandes Siqueira

17 Questions 32 Answers 0 Followers

Questions related from Arthur Fernandes Siqueira

In your opinion, what are the basic skills necessary to a bioinformatician?

Inside the Computer Science and Biology fields.

02 February 2013 9,560 9 View

How do I get a gene list of fully sequenced and assembled genomes? (~9Mpb)

I want to perform a simple comparison test between 3 genomes, build a Venn diagram to analyze the percentage of common, exclusive and different genes among these 3 genomes.

01 January 2013 4,823 4 View

What is a good definition for "critical genes"?

For example: Genes responsible to nitrogen fixation in Rhizobia, genes responsible for photosynthesis in A. thaliana etc. They are classified as critical genes, right?

01 January 2013 1,125 2 View

How to use order as profile level in STAMP?

I have my metagenome uploaded in MG-Rast. How can I download the data and use "order" (level) in STAMP to run statistical analysis?

12 December 2012 1,850 0 View

It's possible to have two substrate binding protein domains in a single ABC transporter?

I have found it in a bacteria genome during an analysis in slilico. Thanks, Merry Christmas and Happy New Year.

12 December 2012 2,471 4 View

Using STAMP to analyze metagenome data uploaded in MG-Rast.

I have 3 file types downloaded from MR-Rast. (1) *.FNA, (2)*.TXT, (3)*.RMA. How can I import to STAMP to analyze my data? I know its necessary a Profile and a Metadata archive in STAMP. How can...

11 November 2012 2,581 4 View

How to compute differences among 2 entire and closed genomes?

I have 2 genomes fully assembled and annotated. (9Mb. each, aprox.) I want to do a basic analysis to discover difference (%). Nothing so complex, maybe align these 2 genomes and discover the...

11 November 2012 9,909 11 View

How to validate a hypothetical protein?

If I have a hypothetical protein in my genome sequence (bacterial genome sequence) and I want to do a lab study (not silico analysis) to validate this protein, what are the basics steps to goal?...

11 November 2012 8,212 2 View

What is the difference between "sn-glycerol-3-phosphate" and "glycerol-3-phosphate"??

What means this "sn" means?

09 September 2012 6,454 9 View

What is the better way to express difference between two data tables?

Bar Graph? Pizza Graph? No graph? I have two data tables, but the numbers it's too similar between both, a LITTLE difference occurs in my data. I want to show this for the public. Show can i...

09 September 2012 9,499 5 View

Are putrescine (polyamine) normally present in soil?

I´ve found putrescine transporter in my Rhizobium genome, and I really want to know if polyamines (putrescine mainly) are found in soils or if is only synthetized by bacteria, fungi, plants or...

08 August 2012 1,897 3 View

Are ABC transporter sequences usually organized in cluster in genome?

In my genome I always found ABC transporters organized as side by side genes. Is it a pattern for ATP-binding cassette transporters?

08 August 2012 1,637 3 View

What bioinformatic software can I use to do statistical analysis and comparison of two entire genome sequences?

I have 2 complete genomes sequences (Annotated and Assembled) DNA Sequence and AA sequence too. Thanks.

08 August 2012 1,429 10 View

B. japonicum

Bradyrhizobium japonicum has the pathway to denitrify in absence/low concentration of O2. This is a common process in B. japonicum? Usually in soils have specific bacterias that do this job. I...

08 August 2012 3,876 0 View

Why collect root nodules at the flowering stage?

In many papers, in th material and methods to isolate Rhizobium from nodule, the authors collet nodules at flowering stage. Why? At this moment plants have a high metabolism to develop the flower...

06 June 2012 6,110 8 View

How to define where starts and ends a Symbiotic Island (SI) in Bradyrhizobia genome?

I really have doubts which parameters to use in addition to symbiotic genes (nif, fix, nod...)

05 May 2012 774 0 View

What's the meaning of "Cloning Bias"?

I was reading a paper when I read this sentence: "[...] five random libraries with four types of cloning vectors were constructed from the total cellular DNA to minimize the cloning bias." What...

04 April 2012 5,118 4 View