Is BLAST highly sensitive?

Question

[karakasmenderes6]

Heyy, I have downloaded a fasta mRNA sequence from NCBI and it is an aquaporin of Milnesium tardigradum. There is a relative species is Hypsibius dujardini and it has a complete genome sequence. I searched this mRNA in blast and it didnt find any similatities between genome and mRNA. This happen a lot. I assume that some basic proteins are universal like the proteins that involve in glycolisis and I expect to find similarity in every whole-genome Sequenced organisms. So is this totally normal?

[fishgolden]

So is this totally normal?

Yes. Searching similar nucleotide sequences are really difficult because there are only 4 different types of letters in general. Which variants of BLAST did you use? Using tblastx https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&BLAST_SPEC=&LINK_LOC=blasttab , you may find some hits with your query.

[karakasmenderes6]

when I use blastx there are some results but none of them related to aquaporin. I know that whole genome of Hypsibius dujardini is sequenced definitely but blast find any similarities. I mean there is whole genome and there is my mRNA which is transcribed from a gene and this gene is in the genome so why can't I find any similarities ?

[fishgolden]

I mean there is whole genome and there is my mRNA which is transcribed from a gene and this gene is in the genome so why can't I find any similarities ?

I might misunderstand what you are talking but, the genome of Hypsibius dujardini looks that is not booked in refseq_genomes db.
I think there were a db named "chromosome" but I can't find it now.
Try wgs or some other dbs.

Answer 1

[GenoMax]

BLAST is pretty sensitive in locating homologs/orthologs/paralogs but a lot depends on how one does the search, parameters used for search, if you are searching with protein (preferred) or DNA etc. Did you try to restrict your blast search (if you did the online one) to just Hypsibius dujardini ? Which accession number are you looking at?

[karakasmenderes6]

JN378746.2 Milnesium tardigradum aquaporin 11 (AQP11) mRNA, complete cds I searched similarities between this sequence and all sequenced Hypsibius dujardini genomes. I just write blast genomes section name of the species so I guess in this way I restricted the search just Hypsibius dujardini and there was no result. I guess all tardigrades have aquaporins but why didn't it find any similarities ?

[GenoMax]

If you do this search at the nucleotide level then even using plain blastn that allows for somewhat similar sequences option most of the hits you get are short (Search Link, Will expire in a couple of days).

With translated search we fare better. Take a look at this search where there is a hit to an aquaporin. Top hits could potentially be aquaporins as well. (blastx search link, will expire in a couple of days).

[karakasmenderes6]

I am really thankfull, from now on I will use blastx for my searches.

[GenoMax]

Consider the context of analysis you are doing and then select an appropriate method based on that.