search

snayfach / MIDAS

An integrated pipeline for estimating strain-level genomic variation from metagenomic data
http://dx.doi.org/10.1101/gr.201863.115
GNU General Public License v3.0
124 stars 52 forks source link

Request for information on how are marker genes chosen in custom database ? #131

Closed Aiswarya-prasad closed 2 years ago

Aiswarya-prasad commented 2 years ago

I am using midas on my custom database comprising my own MAGs. It is not clear to me what criteria are used to select marker genes. Is it just that they should be core (present in all MAGs) of a given species? Are there any relaxations or further contraints to this?

snayfach commented 2 years ago

The marker genes are listed here: https://github.com/snayfach/MIDAS/blob/master/midas/build/phyeco.hmm and described in the paper. They are a list of 15 universally distributed, single copied, protein coding gene families. Let me know if you run into any issues with the database building.

snayfach commented 2 years ago

I should add - those 15 genes are identified in the genomes you provide as input.

Aiswarya-prasad commented 2 years ago

Is this done in a data-dependent way? Meaning that the same genes be searched for in any genome or are they 15 genes that happen to be in the given database? I also find that there is a different number of marker genes for each species-id group.

snayfach commented 2 years ago

Each of the 15 genes is represented by a profile HMM and those HMMs are what's searched against a new genome when you do a custom database. All 15 should be found in any new bacterial/archaeal genome, provided they are near-complete.

On Sat, Oct 15, 2022 at 1:08 PM Aiswarya @.***> wrote:

Is this done in a data-dependent way? Meaning that the same genes be searched for in any genome or are they 15 genes that happen to be in the given database? I also find that there is a different number of marker genes for each species-id group.

— Reply to this email directly, view it on GitHub https://github.com/snayfach/MIDAS/issues/131#issuecomment-1279824220, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQBXLO6WVVUH6CVM3XU5ATWDMFK5ANCNFSM6AAAAAAREDGUI4 . You are receiving this because you modified the open/close state.Message ID: @.***>