NCBI_NOW lecture 1 question on SRA blast

Question

[rgmilian]

Hi, in lecture 1 you do a blast aligning SRA sequences from Mus with human IFNg- why didn't you use the mouse IFNg instead to do the alignment?

Thanks

Rolando

[DCGenomics]

Excellent point, I totally should have.

Good catch!

Ben

[rgmilian]

Thank you!

Regards,

Rolando

Answer 1

[Antonio R. Franco]

It depends upon the goal..

For example.. You can define as task a dc-megablast search to look for orthologous sequences within your sra file

You can find interesting the fact that sometimes you don't find anything interesting with a regular blastn when something appear when playing with different tasks or word sizes and gap and extension penalties. And this is something you only can accomplish if using a orthologous sequence