Find top 5 The Tolerance Identification API finds the top N closest (by blosum62Blosum62) 9mers N-mers in the human genome against your a given protein of sequence of interest.
https://github.com/CyrusBiotechnology/tolerance-identification

Running tolerance-identification

cyrus submit tolerance-identification NLYIQWLKDGGPSSGRPPPS --top-n 10

Inputs:

...

top-n: Collect top-N matches (defaults to 20)

...

Quickstart

Get the top 10 closest 9-mers:

cyrus engine submit tolerance-identification NLYIQWLKDGGPSSGRPPPS --top-n 10

Get the top 5 closet 9 and 15-mers:

cyrus engine submit tolerance-identification NLYIQWLKDGGPSSGRPPPS --top-n 5 --nmer-sizes 9,15

Inputs

• --sequence (str)

  • Input protein of sequence to compare against

Options

• --top-n (int)

  • Collect the top N matches

  • default = 20

• --nmer-sizes

  • Nmer size(s) to run this on (Comma separated string ex: 9,10,11,12)

  • default = 9

Outputs

• out.csv

  • CSV file containing the following columns

    • nmer_size - size of this nmer

    • resnum - residue number (1 indexed) of the nmer position in the query sequence

    • query_seq - query sequence

    • matchrank - Rank (0=best, N = worst ) out of the top-N closest (by blosum62) nmers to the query

    • matchscore - blosum62 score of the result to the query sequence

    • matchseq - the found human genome sequence

    • matchscore/max_score - matchscore divided by the score of a 100% (normalized Blosum62)

• out.json

  • JSON format of the out.csv

Notes

Input proteome

The input proteome file was taken from https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.abinitio.fa.gz