BLAST

[SteveF008]

I'm looking for a little help or just confirmation on whether or not the results I'm getting from BLAST mean anything or if I am completely not usiing this tool properly.

 

I am using a sponge sequence Geodia neptuni 18s ribosomal RNA gene, complete sequence GI = 53771873

 

and running a nucleotide blast against all bacteria and get this result; 92TUW20U01R

 

A score on the alignment of 1459 and 82% identity with the bacterial sequence identified as Azotobacter vinelandii is far better of an alignment than blasting that bacteria against all other bacteria.

 

That doesn't seem right to me.

[SteveF008]

Updated result link 96TDR7FH01R

[CharonY]

Note that blast links are only maintained for a limited amount of time. But it is not terribly surprising that using blast you could get hits to bacterial 16srRNA (which I assume is what you got). After all, the sequences are very conserved. However, if you are saying that if you blast bacterial sequences they are more similar than that of Geodia to bacteria then something is wrong. Is the bacterial sequence you used well annotated (or only partial, environmental isolate, etc?). Typically you would expect maybe around 15-25% deviation from the next best 18sRNA and maybe 1% from other bacterial sequences (roughly).

 

Edit: crossposted

Edited January 11, 2016 by CharonY

[SteveF008]

I put up an updated BLAST result link, here it is again 96TDR7FH01R. I apologize for my ignorance here but I'm taught at using this tool, in fact I'm self taught in general on this subject, but I try. It's an 18s gene I thought it would be 16s. Here is the hit

 

Azotobacter vinelandii isolate DNA101014 18S ribosomal RNA gene, partial sequence

[CharonY]

Uh, there is something wrong if a bacterial isolate has a 18s rRNA... But other than that, do you have a specific question?

[SteveF008]

The main question was why that bacteria was aligning better with the sponge than with other bacteria, but I would appreciate guidance on isolating bacterial strains from sponge genomes, is that pretty straight forward or something that would take a lot of time explaining? I know how to find the sponge genomes, does this require primers?

[CharonY]

I do not think that is the case. Take the 16s rRNA sequence from any bacteria, run against nt and you will only find bacterial hits.

[SteveF008]

Okay let me get away from bacteria and use two organisms with an 18s rRNA sequence Using a diatom sequence Phaeodactylum tricornutum genomic DNA containing 18S rRNA gene, strain M17

 

compared to sponges gets this reult; 97431TCR013, a total score of 1775 with 87% identity, considering the e-value is 0, would you consider this a very significant alignment? Thanks

Edited January 11, 2016 by SteveF008