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Stable version: 2.2.1
TMSEG is a tool which predicts transmembrane proteins, and their transmembrane helices and topology.
Compatible with Java 8 (current release) and Java 7.
- Download and install git lfs
- Linux : Unzip, double click install.sh.
- Windows : Install from .exe
- See git lfs wiki for help during installation
- Complete installation
- Linux: $ git lfs init --> should return "git lfs initialized"
- Windows:>git lfs install --> should return "git lfs initialized", >git-lfs --help --> should return the help documents
- Clone the repository
- Installation is ended!
The TMSEG input requires evolutionary data in the form of a PSSM, typically generated via PSI-BLAST.
Detailed instructions for PSSM generation are currently available on the RostLab TMSEG Wiki.
To run the project, please use the following command:
java -jar tmseg.jar -i examples/query.fasta -p examples/query.pssm -o query.out
- -i Input FASTA file/folder
- -p Input PSSM file/folder
- -o Output file/folder (human readable)
- -r Output file/folder (raw prediction scores)
- -m FLAG if set, do multi-job (interpret input/output paths as folders)
- -x FLAG if set, a previous prediction is processed (must be supplied in FASTA file)
- -t FLAG if set, only the topology prediction is performed (-x must be set)
For the preceeding query, you are supposed to have in your query.out file:
# SEGMENT START END RI
##
# OUTSIDE 1 9
# TRANSMEM 10 34 8
# INSIDE 35 79
# TRANSMEM 80 102 8
# OUTSIDE 103 121
[...]
>sp|Q60019|NQO8_THET8 NADH-quinone oxidoreductase subunit 8 OS=Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) GN=nqo8 PE=1 SV=1
MTWSYPVDPYWMVALKALLVVVGLLTAFAFMTLIERRLLARFQVRMGPNRVGPFGLLQPLADAIKSIFKEDIVVAQADRFLFVLAPLISVVFALLAFGLIPFGPPGSFFGYQPWVINLDLGILYLFAVSELAVYGIFLSGWASGSKYSLLGSLRSSASLISYELGLGLALLAPVLLVGSLNLNDIVNWQKEHGWLFLYAFPAFLVYLIASMAEAARTPFDLPEAEQELVGGYHTEYSSIKWALFQMAEYIHFITASALIPTLFLGGWTMPVLEVPYLWMFLKIAFFLFFFIWIRATWFRLRYDQLLRFGWGFLFPLALLWFLVTALVVALDLPRTYLLYLSALSFLVLLGAVLYTPKPARKGGGA
222222222HHHHHHHHHHHHHHHHHHHHHHHHH111111111111111111111111111111111111111111111HHHHHHHHHHHHHHHHHHHHHHH2222222222222222222HHHHHHHHHHHHHHHHHHHHH111111111111HHHHHHHHHHHHHHHHHHHHHHH222222222222222HHHHHHHHHHHHHHHHHHHHHH1111111111111111111111111111HHHHHHHHHHHHHHHHHHHH22222222HHHHHHHHHHHHHHHHHHHHHHH1111111111111111HHHHHHHHHHHHHHHHHHHHHH2HHHHHHHHHHHHHHHHHHHHHH11111111111
The first part tells you how is the protein segmented, the second gives you the name of the protein.
Residue Annotations in TMSEG output
- N : not a membrane protein
- S : signal peptide
- 1 : intracellular
- H : transmembrane helix
- 2 : extracellular
see [This chart](Application Flow.pdf)