lyok

Hallo all,

I was wondering how CO₂ works to sedate animals?

I can imagine that the lack of oxygen (or the fact you have more CO₂ in your body than needed) can have an influence  , but how exactely does this work?

Dear all,

I have a simple question: the NCBI "16S ribosomal RNA sequences (Bacteria and Archaea)" database contains DNA sequences of the 16S RNA gene right?

My confusing start because of the name: 16S ribosomal RNA sequences, but those are not RNA sequences, right?
(since I can use DNA sequences to blast in that database I assume its DNA or the 16S rRNA gene)

or am I missing something here?

Dear all,

can someone explain to me in simple english wat non redudant database means?
(in relationship to the ncbi non redudant nucleotide database).

Does it mean that each sequence is just 1 time present in the database? or?

And if so: how does this work when you get your results? I mean: if you get a hit with a known sequence from the database its a hit with just 1 sequence and not the "redudant" ones, but does this mean you will not get the other sequences as hits?
Eg: I blast the sequence AATTGGCCC with the non redudant database and I get a hit with the same sequence in B. cereus , but for example E. coli has the same sequence, will I still know this since the sequences are seen as redudant?
I suppose it will show up ?

thanks in advance.

Dear all,

I would like to blast/compare a sequence (one that I have) with one that is avaible on ncbi.
How can I do this in the most elegant way?

The problem is that I do not seem to find a way to download the entire sequence to use it on http://blast.ncbi.nl..._SPEC=blast2seq
(blast2sequences)

When I download the fasta format of the organism from ncbi I get a file with all the contigs, however they are interupted with
">gi|381420886|gb|AFNH02002571.1|  contig03417, whole genome shotgun sequence" statements".
(statement sequence statement sequence.. it goes on like that rather then having 1 big sequence taped together)
So when I try to copy and paste the genome into the website it only checks the first sequence with my sequence rather then checking the entire sequence.
Is there an alternative to check my sequence with the one form ncbi?
Or is there an easy way to remove those statements from the file?

Dear all,

I have been offered the oppertunity to do a PhD.
Which is great, I always wanted to do this, however this is a big but!

The problem is that the goal of the PhD is more likely not achievable.
What I mean is very simple: the aim/goal of the PhD is something that might not work at all.

I now wonder: should I go for it or not? What if I stay for 4 years (length of PhD here) and end up with pretty much no "real" results?

The PhD is something completely new and the changes are I will not be able to do what it aims for because a lot has to be done prior to really starting the research.
So its possible I end up with a lot of "small" results about preparations and not really with a clear, good, result.

Any advice?


I wonder: is it even possible to get your PhD degree if you dont attain the end goal? Because in the end: you cant really know up front if you can achieve it.