HGT detetction in fish

[posavi28]

Hi Qiyun,

I've tried to use HGTector to look for HGTs in 4 fish species using the pre-built default database. While search worked OK I didn't get any close and distal hits when running 'hgtector analyze' . I am attaching the head of scores table (>850,000 rows).
1 sample protein length hits self close distal match
2 P_annectens_all_prot EDL42285.1 421 2 1.34624 0 0 0
3 P_annectens_all_prot EDL42286.1 445 3 1.71551 0 0 0
4 P_annectens_all_prot EDL42287.1 527 3 1.50798 0 0 0
5 P_annectens_all_prot EDL42288.1 534 3 1.60766 0 0 0
6 P_annectens_all_prot EDL42289.1 451 3 1.68074 0 0 0
7 P_annectens_all_prot EDL42290.1 198 8 3.40867 0 0 0
8 P_annectens_all_prot EDL42291.1 245 4 1.7295 0 0 0
9 P_annectens_all_prot EDL42292.1 721 3 2.04885 0 0 0
10 P_annectens_all_prot DL42293.1 447 3 1.45622 0 0 0

Please let me know if you have any suggestion how to run HGTector to detect HGT in fish. Is it possible to detect HGT in fish by HGTector?

Thank you.

Marijan

[qiyunzhu]

Hello @posavi28 Thanks for your interest and sorry for the late response. The default database is for microbes only. It won't work with fish (It isn't common that fishes exchange genes...). But you can build a database that contains vertebrate species with:

hgtector database -o fish --cats vertebrate_other --sample 1

You may further add --taxids 7898 so that it only contains ray-finned fish species (Actinopterygii).