Orthology prediction among 900 genes taken from whole taxonomic tree

Question

[Naresh]

I have taken around 900 genes from whole taxonomic tree. Now, I am interested to find the Ortholog among those 900 genes. Please guide me.

Answer 1

[k.kathirvel93]

you mean, you want to predict COG?

Answer 2

[xinwangcau]

You could use OrthoMCL to find the ortholog among 900 genes.

Answer 3

[k.kathirvel93]

Here is the Link to get orthologs : http://weizhong-lab.ucsd.edu/metagenomic-analysis/server/cog/

Answer 4

[ta2007]

Sorry but your question isn't very clear. How many species do you have? Do you want to find orthologs among these species? You can use a new tool called OrthoFinder. It is very easy to install and run. It takes protein files and finds orthologs using all-versus-all blastp searches. I highly recommend that you name your files in a specific manner such as genu_spec.pep --- 4 letters for genus and 4 letters for species. And within each pep file, you should name your headers like genu_spec_n. This will make your life very easy for downstream analysis because OrthoFinder randomly chooses parts of the header from each file and adds it to the file name. This becomes your new header in the files that contain orthologs. So having files that are named the same way is very helpful no matter what you do with the orthologs. I learned this the hard way. I hope that helps!

Answer 5

[natasha.sernova]

Where did your tree come from? Do you know how it was created?

I would start from the very beginning, You search for orthologs, am I right?

I would recommend another very useful program, OMA, OrthologousMAtrix.

It is very user friendly.

It requires

1) several protein *.fa files, one for each species, in its database DB

(you create this database enumerating all your species as *.fa-files)

to let the program find orthologs between them, and

2) parameter-file - that's it. There is a default parameter file,

so you even don't need to worry about.

http://omabrowser.org/standalone

References are inside the web-site above.

Good luck!

Answer 6

[Naresh]

Archapteryx software through which it was created. I have collected some randomly genes from Human, Protozoa, Fish, plants and fungi. around 900 genes from NCBI database.

Now, I want to find the ortholog among those genes in order to interpret the evolutionary relationship between all these genes?

So, As you all mentioned above the software, I need to get the FASTA sequence of the genes. which is tedious to get for 900 genes.

I wanted to know any software which will find ortholog among these different species by genes, not protein sequences.

Pls correct me if i am wrong