Maker Annotation - multiple gene models give same blastp match

Question

[MH85]

Hi everyone,

INTRO: I have completed genome annotation of nonmodel organisms (fish) using MAKER. After three runs of MAKER, I filtered protein.fasta removing all with AED > 0.5 and I BLASTed these against SwissPort: blastp -evalue 1e-6 -max_hsps 1 -max_target_seqs 1.

PROBLEM: I got quite a lot of cases when two or three gene models have the same blastp match i.e. same hypothetical product. Some of them are next to each other in the genome and I assume that this is due false presence of start/stop codons within the gene span, but others are completely separate.

QUESTION: What causes this? Is it a problem with assembly? And how to correctly fix this issue?

Thanks a lot, Milos

[jean.elbers]

First thought, these are probably paralogs. Also just as a reminder, you should Google about -max_target_seqs 1 with NCBI blast+ in general, as it does not produce the "best" match always.

[MH85]

Thank you!!! I had no clue about this issue with -max_target_seqs 1 before.