Finding homologs in BLASTN

Question

[Meeeee]

Hi! I am trying to find homologs using BLASTN within an assembly, however I don't understand why do I have different ranges of my query in my subject but in different genome positions. Also, how to read the alignment of these ranges with my query sequence as there are many.

Thanks! Im new to this :(

[GenoMax]

blast+ as the name says is a local aligner. So it tries to find local alignments between query and the database sequences. These local similarities result in high scoring pairs (HSP's) like the ones you see above. There may be multiple HSP's in a single subject sequence (especially a chromosomes). You should read this document from NCBI to understand how BLAST works. Note: It is marked for historical reference but explanation of how a BLAST search works is still valid.

Note: If you are trying to find homologs then it is always better to work in realm of protein sequence than nucleotide.

[Meeeee]

Thanks! So as I did with proteins, should I choose the hsp with the higher scores and less e value?

[GenoMax]

should I choose the hsp with the higher scores and less e value?

Without knowing what the query is and what you are trying to do I can't say. HSP with high scores and low e-value are indeed similar/homologous but they could simply be matching a domain (or a functional site, motif) in a bigger protein which otherwise may not be homologous to whatever you are searching with.