I found similar domains of wood genes of a species with the domains of other species. How can I know that these are same genes?

More Neha Goel's questions See All

I had minimise the energy of protein, still I don't have good procheck value, verify-3D value please suggest to me what I should do?

10 November 2013 7,690 9 View

Can anybody tell me about the insilico tool to validate the identified gene.

I have some common domains in targeted genome and reference sequences of wood. What should I do to find the gene through these domains?

01 February 2013 691 1 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

Useful architecture for bioinformatics?

Hi Dear researchers In ensemble-based architectural design Which algorithms are more useful for classification? What is the difference between parallel and ensemble architecture? Thanks I am...

08 February 2021 2,727 5 View

Electron density difference maps(Fo-Fc): what is the meaning of negative densities (red blobs)?

Dear community, As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data. However, in many cases (e.g. attached image), when...

06 February 2021 2,847 2 View

Qiime2- No reads passed the filter. How to set the trunc value?

Hi, I am working on some 16S sequencing data, and seems some of them are low quality. I am not sure how to set the trunc value in dada2. qiime dada2 denoise-paired \ --i-demultiplexed-seqs...

30 January 2021 6,213 3 View

Which software to use to statistically analyze Telomere Length_TRF_Southern Blot?

I am trying to measure telomere length in an ant species using the TRF method, which is a Southern blot technique. Currently, I am struggling with analyzing the images and would appreciate any...

29 January 2021 604 3 View

MHC Rabbit Genome Annotation? Domain annotation of each MHC Rabbit Gene?

I want to find a database(s) or a method where I can find and bulk download all the rabbit MHC genes and domain annotation. In humans using Ensembl, all MHC genes have names and domains but in...

28 January 2021 7,722 2 View

Best tool to build missing residues, minimize and validate a ligand model?

I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands! what I need is to connect them...

23 January 2021 3,975 7 View

What's the role of bioinformatics in poultry science?

bioinformatics has a big importance in human science and lots are seeking to study that field, so it attracts me to know it's relation with poultry science and how we can benefit from it in...

20 January 2021 6,963 3 View

How can I get the chromosomal location of a list of genes?

I'm looking for a bioinformatics website to get the chromosomal location of a radish gene id list, but in one shot instead of doing it gene by gene. Is there a way to do this? Thanks

17 January 2021 8,810 3 View

Om Prakash Sharma

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..

Neha Goel

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.

Harsh Dweep

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?

Logambiga Prakash

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??