BLAST usage (conserved domains, ortholog sequences and pssm profile)

Question

[Jimpix]

HI! I need help with BLAST, It seems not to be hard but I have never done that. First I need to search by gi: 126302547 related protein sequences limited to chordata (what was typed). When I run BLAST in the table below I see sequences from any organisms. What is the problem? Then I need to define conserved domains, select a ortholog sequences and build a PSSM profile for them. Please kindly, advise me.

Answer 1

[Mensur Dlakic]

This sounds like homework, and it is very doable as most steps are (semi-)automatic with BLAST. I will give you some hints.

It is really not that difficult to find what chordata are: all organisms with some kind of a dorsal (on the back) nervous system. That includes many organisms, so it is not surprising that you get many hits.

You can find about conserved domains database with a simple Google search. I am listing a couple of relevant links below:

• https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
• https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

For the rest I suggest Googling on your own.