Is ther a tool to compare protein identities between two nearly identical proteomes?

Question

[zack.saud]

Hi all,

I'm looking for a tool to compare two fungal proteomes. The proteome set consists of around 11,000 different proteins each that were predicted in-silico from two sequencing experiments. One is from a parent fungal strain, the second proteome is that of the parent strain after passage in culture. There are phenotypic changes in the organism after passage, so I'd like to know which of the proteins between the two sets are different from one another. I've done a protein blast but it is still a big task to go through the blast output to see which proteins don't have 100% identity and coverage.

Is there a tool that could make me do this quicker?

Many thanks in advance

Answer 1

[Mensur Dlakic]

If you need to know this for individual proteins, what you are doing is probably a way to go. It is very difficult to find this from pairwise BLAST alignments, but very easy if you use the output format #6 (option -outfmt 6) and sort the whole output by the alignment mismatch (I think that's the 5th column).

If you are interested in average amino-acid identity between genomes:

• https://github.com/faylward/lastp_aai
• https://academic.oup.com/nar/article/46/W1/W479/4995691

And you may want to know average nucleotide identity as well because it is easy enough:

• https://github.com/ParBLiSS/FastANI
• https://github.com/widdowquinn/pyani

[zack.saud]

Hi,

This answer is more than I hoped for... thank you for the info, I really appreciate it.

Best