454 assembling against reference genome

[donniemarco]

Hi,
Can anyone please let me know from where I can download "Reference Sequence" that I can run against BLAT. I came across this term quite too frequently but I am unsure which file might be the correct.
Regards!!

[nilshomer]

Hi,
Can anyone please let me know from where I can download "Reference Sequence" that I can run against BLAT. I came across this term quite too frequently but I am unsure which file might be the correct.
Regards!!

You should be able to find a reference genome for your species of interest at the NCBI website.

[westerman]

Finding the proper reference sequence is one of my biggest headaches. But then our facility deals with off-beat genomes.

Nils is correct that NCBI is a good bet to get your reference. But often the species specific web sites often have a more up-to-date reference than NCBI. Additionally different groups will annotate the same species in different ways. Thus there can be multiple web sites out there producing varying references.

I have now gotten to the point where I insist that the researcher (for who I am working) give me the *exact* web page where I can download their reference. None of the "oh, just assembly 4 of my desired species."