Hi everyone, i would like to know if there is a software or a website to compare the amino acid content of many sequences. I explain: i did a mass spec analysis, i wanted to see proteins that aggregate in a specific condition and now i want to know if there is a way to compare all this sequences to know if they are for exemple containing more histinine, cysteine ...than the ones that do not agggregate?
like a expasy ProtParam tool but for multiple sequences
I have used Jalview before to form alignments of a few proteins, less than you are. I was able to fit everything onto one page, by just wrapping the text. I think if you want a very robust alignment you should probably consider using MEGA. You can get some stellar phylogentic trees from an alignment file that you create using your sequences in the program: https://www.megasoftware.net/
If you got such short bursts of amino acid sequences you should probably use a local alignment, as opposed to a global alignment. I think the MUSCLE alignment method is the best which is available in both of the softwares I believe.
Here is a little alignment I made in Jalview. I wasn't just aligning random proteins. The proteins are functional homologous. You can even get those fancy probability distributions of single letter amino acids. It's a local alignment with gaps for where nothing matches. Probably download the image and zoom in and out to see it better.
I've used Clustal and Blast and had a positive experience with both. User friendly and intuitive to learn. Best of luck.
Clustal Omega: https://www.ebi.ac.uk/Tools/msa/clustalo/
Protein BLAST:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=bl
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