chromosome comparison

[sadiexiaoyu]

Dear All,

I would like to ask is there any software can compare two chromosomes? For example, if I want to see how many genes are orthologues in one chromosome in Human and one chromosome in mouse?

Besides, is there any software can detect for example, how many genes from one chromosome of mouse have common ancestor with human chromosome? And which chromosome of human are these genes in mouse chromosome orthologues from?

I hope that I express it clear... It is a new area for me, welcome for any suggestions!

Best,

Sadiexiaoyu

[GenoMax]

Mouse Genome Informatics (MGI) is the perfect resource for this. You can find the information you are asking for as plain text files here: http://www.informatics.jax.org/homology.shtml

[sadiexiaoyu]

Dear GenoMax,

Thanks for your reply.

But I would like to not only compare chromosome between mouse and human, but also for other species which are not included in the list in the website... I think maybe I need to extract the whole chromosome and compare them by myself...I don,t know whether there is software can help me do that...?

[GenoMax]

UCSC has precomputed pairwise and multiple-alignments available for multiple species (e.g. http://hgdownload.soe.ucsc.edu/downloads.html#human).

Ensembl has compare genes across species and alignments: http://www.ensembl.org/info/website/...s/compara.html

[sadiexiaoyu]

ahha, this is really helpful!

But another question... is there any convenient way to view the alignment results? For example, which part of the chromosome of the species have common ancestor as which part of the chromosome of human being?

[GenoMax]

I am not aware of a comprehensive resource that can display this at chromosome level. I came across this paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031395/) that you may find interesting.

You can see gene-centric multiple sequence alignments in Homologene part of NCBI (e.g. http://www.ncbi.nlm.nih.gov/homologene/41).

[sadiexiaoyu]

Thanks for these suggestions!

[sadiexiaoyu]

Is there anybody know how to make syntenies for chromosomes from different species?

[maubp]

MAUVE might be useful here, at least for smaller genomes:

http://darlinglab.org/mauve/mauve.html