Question: Annotate A Genome With A Well Annotated Related Species
2
gravatar for Nicolas Rosewick
8.0 years ago by
Belgium, Brussels
Nicolas Rosewick8.8k wrote:

Hi,

What is the easiest way to annotate a genome that has no annotation. I've the genome and annotation of a very related species.

In final, I wan to have the same structure as refGene.txt and ensGene.txt from UCSC.

Here's an example from the RAT ensGene.txt :

585    ENSRNOT00000044270    chr1    +    5472    16844    5472    16844    8    5472,5523,8281,8991,10768,14683,15968,16733,    5485,5725,8567,9795,10993,14807,16732,16844,    0    ENSRNOG00000021490    incmpl    incmpl    0,1,2,0,0,0,1,0,
585    ENSRNOT00000049921    chr1    +    5525    16968    5525    16968    8    5525,8275,8991,10768,14677,15965,16733,16943,    5725,8567,9795,10993,14807,16732,16846,16968,    0    ENSRNOG00000021490    cmpl    incmpl    0,2,0,0,0,1,0,2,
585    ENSRNOT00000051735    chr1    +    5525    16968    5525    16968    7    5525,8275,8991,10768,15965,16733,16943,    5725,8567,9795,10997,16732,16846,16968,    0    ENSRNOG00000021490    cmpl    incmpl    0,2,0,0,1,0,2,

My strategies is to download all the gene (CDNA ?) from ensembl and ucsc from this related species and to map with gmap them on the unannotated genome. Is it a good way to do this ?

Thanks a lot,

N.

genome annotation • 1.6k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 8.0 years ago by Nicolas Rosewick8.8k
3
gravatar for Lhl
8.0 years ago by
Lhl730
United States
Lhl730 wrote:

yes, basically you can follow the similarity-searching-based (map proteome of relative species to your genome assembly) method. And you can also try some de novo gene prediction approaches. Then, it is good to combine the two different strategies (this can be done using some combiners, e,g,, EVM, glean, Maker ...).

ADD COMMENTlink written 8.0 years ago by Lhl730
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 982 users visited in the last hour