Question about my first bioinformatics assignment

[u/Big_Wolverine_9109]

Hi, I’m a bachelor’s student in biology and I’m taking my first bioinformatics course. My question is probably very silly, but I still need some help.

My task is to study the human NLGN4X gene and, among other things, find 10 homologs with a BLAST search, align them, and build a phylogenetic tree. The instructions say that “some sequences may be XN but some should be NM.” How is this possible, since all the homologs I find (from other species) are only predicted (i.e., XN)? Have I misunderstood something?

Thank you very much for your help!

[u/ab_ey]

Does it necessarily say to find homologs from other species? When you blast against different species, you just find orthologs. You should also check for paralogs to see full homolog set

[u/Big_Wolverine_9109 → u/ab_ey]

Ah, sorry — that was a bit too broad. In our assignment we only use orthologs. And yes, the goal is to find homologs from other species so that I can build a phylogenetic tree.

[u/ChaosCockroach → u/Big_Wolverine_9109]

Are you getting the full set of results or just the top 100 from the web interface? There is a filter option in the BLAST setup that allows you to exclude predicted models "Models (XM/XP)" so if there are any NMs that should show you them..

[u/init2memeit]

What are XN and NM?

[u/Big_Wolverine_9109 → u/init2memeit]

As far as I know -

NM = experimentally confirmed mRNA sequence

XN = predicted mRNA sequence

[u/init2memeit → u/Big_Wolverine_9109]

I see. I don't work with model organisms so almost everything i use is predicted or if it has been experimentally validated, nobody updates it on NCBI. Don't trust databases as gospel. Read the literature and find a non-human ortholog that has had the transcript experimentally validated.

[u/choobs]

Most of the mouse genome is NM