smallproteins: Small Proteins

BiBTeX reference:

@article{Hemm.Rudd2008,
author = "M. R. Hemm
 and B. J. Paul
 and T. D. Schneider
 and G. Storz
 and K. E. Rudd",
title = "{Small membrane proteins found by comparative genomics and
ribosome binding site models}",
journal = "Mol Microbiol",
volume = "70",
pages = "1487--1501",
pmid = "19121005",
year = "2008"}

PubMed 19121005
DATA. This is a list of potential ribosome binding sites and potential sigma⁷⁰ promoters in intergenic regions of E. coli displayed as sequence walkers.
Final data set 2007 Dec 06: only orfs in the range 10 to 150 codons with the REPs removed.
- smallproteins-list.txt - list of potential RBS sorted from the strongest to the weakest in bits.
- samples - regions displayed as sequence walkers. This is a large set of postscript and corresponding pdf files. There are also files that contain the detailed features for each location.
- peptidelist.txt - like the smallproteins-list.txt but with peptides listed in two columns for the 1 and 3 amino acid codes. The file is tab delimited. as of 2015 Dec 03
- peptidelist.csv - like the smallproteins-list.txt but a comma-separated variable file (csv) with peptides listed in two columns for the 1 and 3 amino acid codes. as of 2015 Dec 03

  Thomas D. Schneider, Ph.D.
  toms@alum.mit.edu
  https://alum.mit.edu/www/toms

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Schneider Lab
origin: 2008 Feb 03
updated: 2015 Dec 03

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