Compare two proteome

Question

[sontiroy]

I want to do a whole proteome comparison of two organisms. The size of the genome of one organism is around 2.5 Gb and another is 8 Mb. So please suggest me some tools and if it is GUI based on windows it's better.

[Jean-Karim Heriche]

You'll have to be more specific. What kind of comparison do you have in mind and for what purpose ? You want to compare proteomes but you mention genomes. Does this mean that your genomes are not annotated or that you want to compare the protein-coding parts of the genomes or something else ?

[sontiroy]

The genome of both the organism has been sequenced and protein has been annotated. I want to do a comparison to find similarities between the organism at the protein level.

[GenoMax]

Hopefully the protein complements are of a comparable size. That is a huge discrepancy between the genome sizes.

"GUI based on windows" may pretty much eliminate a reasonable chance of finding "a" program that is freely available.

[sontiroy]

Linux based software will also be fine but I don't have much experience in Command line. so I thought it would time consuming. Can you suggest some Linux based software?

[GenoMax]

Have you considered using blastp, blat, DIAMOND. They are all command line programs though.

[sontiroy]

I want to compare 3700 protein sequences to approx 27000 protein sequence. These all have cut off which is way below.

[GenoMax]

These all have cut off which is way below.

Not sure what you mean by that?

[sontiroy]

ok, tell me how to compare proteome of two organisms, one having 3700 protein sequence and another having 27000 protein sequences and find out which proteins are around 90% identical or above .

[Carambakaracho]

blastp or diamond, as genomax wrote is what you need. You won't get a better or easier solution. Choose tabluar outformat and apply excel filters for your thresholds

[GenoMax]

You will search them against each other (using one set as a query and other as database). blat may be the easiest (sounds like you don't want/need evolutionarily distant entities) with -minIdentity=90 option. Use a tabular format so you can parse results if needed.

Something similar can also be done using blastp (if you want more distant relationships) but will be more involved (look into pident option for this) with -outfmt 6.