ROSTLAB

Per-residue and whole-proteome prediction of bacterial transmembrane beta barrels

Introduction	Methods	Download	Prediction

Whole proteome predictions (z-value >= 4.0) README
GramNeg	2056 hits from 78 Gram Negative Genomes
TypGramPos	65 hits from 14 Typical Gram Positive genomes
AtypGramPos	31 hits from 5 Atypical Gram Positive genomes (mycolata)

GenomesGramClass	Gram classification for list of 92 searched genomes


Original Whole-proteome Predictions (deprecated) README.old
proteomes_new_1.hits	1641 hits from 92 genomes, no preexisting annotation, homology annotation threshold e-value = 1.0
proteomes_new_10.hits	1550 hits from 92 genomes, no preexisting annotation, homology annotation threshold e-value = 10.0
proteomes_full_1.hits	3171 hits from 92 genomes, homology annotation threshold e-value = 1.0
proteomes_full_10.hits	3171 hits from 92 genomes, homology annotation threshold e-value = 10.0

Software

All source and binary distributions come with a complete set of input files necessary to do a test run. For an actual run, the user must generate a psiblast profile for the protein sequence of interest.

Source Code and Binaries: proftmb-1.0.tar.gz; proftmb-1.1.tar.gz; proftmb-1.1_linux_bin.tar.gz
Required Third Party Software: opt-3.19.tar.gz; gsl-1.4.tar.gz
GNU/Linux Binary Distro: proftmb-1.0.linuxbin.tar.gz
Apple Macintosh PowerPC OS/X Binary Distro: Sorry, no distribution available.

Data

Complete set of input files for PROFtmb training: Input Files