Why Trace Sequences Could Not Be Found In The Genomes

Question

[jingyun.chi]

I am trying to search some of the sequences I found in the trace archive of NCBI (for example gnl|ti|1332923440 and gnl|ti|1329415412 which belong to the Paramecium tetraurelia) in the genome of Paramecium tetraurelia (Ptetraureliaassemblyv1.fasta). But I can not find any of them. How could those trace sequences be used? Thank you very much!

Answer 1

[Darked89]

The top hit for gnl|ti|1332923440 name:FN0AF182AB09RM1 is

emb|CR933361.1| Spo11-like type II topoisomerase, Paramecium tetraurelia macronuclear gene

In almost any genome sequencing project you can expect gaps in the assembly. On the top of it if (I do not know much about genome structure of Paramecium) quite often reported "genome" may be missing i.e. mitochondrial, chloroplast etc. sequences.

[jingyun.chi]

Thanks a lot! Does that means the trace sequences could be used to find the homology of one gene in the genome? I find 25 sequences with high similarity to the spo11 gene, does it means they are all homology to this gene?

[Darked89]

Yes, you can assemble individual traces corresponding to a gene of interest, or download the whole sets for assembly or mapping to i.e draft genome or related genome(s).