I am not sure neha, but i think genes will be similar. because domain have similar types of folds and structure, and if it is conserved throughout the species. Gene must should be similar only. Please confirm through some literatures or experts..

Om, here I got the same thing as u say from literature. bt they considered through the domain sequnce.they took domain sequence then find in genome..bt here i considered the genome sequence then find the domain.Plz convey your brilliant ideas to me. I will welcome them.

I think its a vice-versa process..both the process are applicable.

May i follow the same procedure... As above i told you

Yes you can move ahead with that protocol!!

Sure, I will try then let u knw.

Hi,

If you are looking for the homologous genes, then you can visit HomoloGene database (http://www.ncbi.nlm.nih.gov/homologene). This database documents homologous genes on 21 different species.

Concerning the similar domains,

Multiple sequence alignment of the similar domains among different species of interest is must. Thereafter, you can define cut-offs of similar genes based on their profiles identity and similarity.

I hope this helps!

@Harsh

Hi, In Homologene db contains the information regarding the crops plants and Mammals. bt i need in forest tree information. I have already found the domains.

As you have already collected information on domains.

Did you check the overall identity and similarity of detected domains of a gene-x among different trees using MSA of aligned profile? If yes, what are the cutoffs?

Dear,

Collect the protein sequence of the domains for the species of your interest. Do MSA with those sequences. If your domains are similar you will get >90% cut off.

To confirm the conserved residues of your domain use evolutionary trace analysis server. This helps you to find out the conserved residues among all your interested species.

@harsh and @ Prakash..I will collect the sequence info of domains then ..i will follow your strategy., thanks

If you have sequence with you go to pfam (http://pfam.sanger.ac.uk/) data base and submit your sequence. It will give you the domain information.

@prakash i have domains information, i am trying to retrieve the squence of domains

overlap identified domains information (start and end position) within your input sequences with the helps of a scripting language eg. PERL (substr function can be used for this task).

@Harsh dweep..I was trying to reterive the domain sequence..When I searched in CDD at NCBI then I got many sequences for 1 domain accession number., on which criteria I have to select the sequences from Db. I also searched on Pfam...there is also same thing with the domain organization..

Hope you have protein sequence for your wood species. Submit it in Pfam..You will be getting multiple domain information with their lengths. Keep the cursor on the domain name of your interest. It will display the range of the sequence(from & to residue number). Using this information you can select the sequence for your domain.

You can retrieve the protein sequence for your wood species from NCBI database

@ Prakash..I had the chloroplast genome of forest tree..and i had the reference sequences of wood from the member of same family, I had develop the ORFs den find the similarity wd the sequences which is more than 90%..now i had the find the domains through CLC workbench..in both target and reference sequnce...i had common 30 domains..now i had downloaded the sequences from Pfam..i am tryiing to find the similarity b/w them..still i am not getting anything., as u told for MSA., Now what should i do??