Hi, I`m working on a proteomic analysis in a product that the composition is not clear.

It is known it contains Pseudomonas strains, however, the MS indicates the presence of protein sequences from other bacteria. I need to find out if these proteins does really belong to other microorganism or are Pseudomonas sequences (maybe the protein sequences are so similar, with only few amino acid differences). I know in the webpage:

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=blasttab&LAST_PAGE=blastn&BLAST_INIT=blast2seq

It is possible to align two or more protein sequences and discover how similar they are.

But the point is, I have >1.000 to compare, which is to much to put in this tool.

Are there any software or tools that alow to do this comparison?

Thanks

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