Tool for assigning putative transmembrane regions in a protein sequence
Reference: 'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins. http://www.ncbi.nlm.nih.gov/pubmed/9183525
SNNS.gbl file contains the neural network created with SNNS (Stuttgart Neural Network Simulator) http://www.ra.cs.uni-tuebingen.de/SNNS/ as explained in the paper above.
Within the same directory simply execute: make
transmem executable will be created.
transmem -w 12 -d Q9BTV4.fasta
This reads Q9BTV4.fasta file with a 12 window size and debugging option.
Lines starting with '#' are debug output and offers information about every residue.
Result lines include separated by tabs:
- IDs of FASTA entries
- a candidate transmembrane stretch of aas
- starting and ending positions within the query sequence.
#sp|Q9BTV4|TMM43_HUMAN@392|R->-1.1 #sp|Q9BTV4|TMM43_HUMAN@393|V->-1.1 #sp|Q9BTV4|TMM43_HUMAN@394|P->-1.1 #sp|Q9BTV4|TMM43_HUMAN@395|A->-1.1 #sp|Q9BTV4|TMM43_HUMAN@396|K->-1.1 #sp|Q9BTV4|TMM43_HUMAN@397|K->-1.1 #sp|Q9BTV4|TMM43_HUMAN@398|L->-1.1 #sp|Q9BTV4|TMM43_HUMAN@399|E->-1.1 sp|Q9BTV4|TMM43_HUMAN GMFVGLMAFLLSFYL 34 49 sp|Q9BTV4|TMM43_HUMAN AAGWMAMFMGLNLM 312 326 sp|Q9BTV4|TMM43_HUMAN LVNIGLKAFAFCVATSLTLLTVAAGWLF 342 370 sp|Q9BTV4|TMM43_HUMAN LWALLIAGLALVPIL 373 388