Question: Id conversion from EGGnog
0
gravatar for fefe
11 months ago by
fefe0
fefe0 wrote:

Hi there,

I'm stuck with a probably simple problem that has nonetheless stole me a lot of time. I still have little experience with this kind of stuff and, although I red similar questions on this and other forums, I didn't manage to solve the issue myself.

I need to do some analyses at both mRNA and protein level on entities linked by paralogy/orthology relationships.
I decided to use the groups identified and classified in EggNOG. I straightforwardly downloaded the protein sequences by using the API but on the site there is no direct way to do the same for the corresponding mRNA (at least to my knowledge). For this reason, I extracted the IDs list that unfortunately is a mix of different notations and it looks like this:

>117187.FVEG_01726T0 
>118797.XP_007458112.1 
>128390.XP_009472214.1 
>12957.ACEP12726-PA 
>132113.XP_003494933.1
>132908.ENSPVAP00000005474

For some of them, it should be possible to use the Entrez E-utilities' esearch/efetch but nonetheless I get errors and the sequences I got downloaded did not match any of the IDs I provided in the file. Since I have >4k entities, it is not reasonable to map them by hand. Could you kindly suggest me a way to work this around? Thank you in advance!

entrez id eggnog • 320 views
ADD COMMENTlink modified 11 months ago by genomax92k • written 11 months ago by fefe0

I straightforwardly downloaded the protein sequences by using the API

Which API are you referring to?

ADD REPLYlink written 11 months ago by genomax92k

The EggNOG's one as I needed to download the fasta, the alignment, and the tree files. Sorry for not being clearer in the question itself.

ADD REPLYlink written 11 months ago by fefe0

Unfortunately the data appears to have come from different sources and EggNOG does not seem to provide a comprehensive list. e.g. FVEG_01726T0 is from Fusarium. You can then find it in Fungi Ensembl. ACEP12726-PA is from Atta cephlotes. I guess there is no easy solution here.

ADD REPLYlink written 10 months ago by genomax92k

Well that's so unfortunate, thank you anyway for trying helping me. Have a happy New Year!

ADD REPLYlink written 10 months ago by fefe0
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: 1203 users visited in the last hour